Simon Jupp Johan Lundin Claudia Lukas Beate Neumann Frauke Neff Thomas Walter Cellular Microscopy Phenotype Ontology cmpo Bran Herpers Jean-Karim Heriche Gabriella Rustici Jennifer L. Rohn Zvi Kam James Malone definition source CMPO subset cmpo Grouping classes that can be excluded Term not to be used for direct annotation Term not to be used for direct manual annotation Aspergillus GO slim Candida GO slim ChEMBL protein targets summary Generic GO slim GOA and proteome slim Metagenomics GO slim PIR GO slim Plant GO slim Fission yeast GO slim synapse GO slim Viral GO slim Yeast GO slim Prokaryotic GO subset Catalytic activity terms in need of attention Systematic synonym Terms created by TermGenie that do not follow a template and require additional vetting by editors Viral overhaul terms subset_property has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym has_scope in_subset shorthand BFO:0000050 OBO_REL:part_of part_of part_of has_part BFO:0000066 external occurs_in occurs_in occurs in quality towards Relation binding a relational quality or disposition to the relevant type of entity. s depends on inheres_in bearer of participates in located in RO:0002092 external happens_during happens_during happens_during RO:0002093 external ends_during ends_during ends_during RO:0002211 external regulates regulates regulates RO:0002212 external negatively_regulates negatively_regulates negatively regulates RO:0002213 external positively_regulates positively_regulates positively regulates transports or maintains localization of has target end location q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 directly_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 increases if the magnitude of q2 is increased, or the magnitude of q1 decreases if the magnitude of q2 is decreased. The relationship is not necessarily linear. cjm 2009-08-26T02:50:08Z quality directly_associated_with Example: 'Lewy bodies increased number related to dystrophic neurite increased number' (from annotation of PMID:8740227 in http://ccdb.ucsd.edu/1.0/NDPO.owl#ndpo_404). Here the increase in the number of lewy bodies is directly_associated_with the increase in the number of dystrophic neurites. Association is weaker than correlation or proportionality. These relations may be later added to PATO. directly_associated_with q1 directly_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 increases if the magnitude of q2 is increased, or the magnitude of q1 decreases if the magnitude of q2 is decreased. The relationship is not necessarily linear. PATOC:cjm Wikipedia:Association_(statistics) s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. quality has_cross_section Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has_cross_section s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. PATOC:CJM quality has_dividend_quality has_dividend_quality quality has_divisor_quality has_divisor_quality quality has_ratio_quality has_ratio_quality q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased_in_magnitude_relative_to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 inversely_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 decreases if the magnitude of q2 is increased, or the magnitude of q1 increases if the magnitude of q2 is decreased. The relationship is not necessarily linear. cjm 2009-08-26T02:50:24Z quality inversely_associated_with Association is weaker than correlation or proportionality. These relations may be later added to PATO. inversely_associated_with q1 inversely_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 decreases if the magnitude of q2 is increased, or the magnitude of q1 increases if the magnitude of q2 is decreased. The relationship is not necessarily linear. PATOC:cjm Wikipedia:Association_(statistics) q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. quality reciprocal_of There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal_of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. PATOC:CJM q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality similar_in_magnitude_relative_to similar_in_magnitude_relative_to q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM has accuracy has qualifier protein polypeptide deoxyribonucleic acid molecular entity nucleic acid macromolecule A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. cell in vitro The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets. GO:0016359 mitotic chromosome segregation mitotic sister-chromatid adhesion release biological_process GO:0000070 mitotic sister chromatid segregation The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets. GOC:ai GOC:jl The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis. Reactome:REACT_101162 Reactome:REACT_1590 Reactome:REACT_29795 Reactome:REACT_34060 Reactome:REACT_78665 Reactome:REACT_78866 Reactome:REACT_83686 Reactome:REACT_91654 Reactome:REACT_93384 Reactome:REACT_93574 G1 phase of mitotic cell cycle biological_process GO:0000080 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic G1 phase The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis. GOC:mtg_cell_cycle Reactome:REACT_101162 G1 Phase, Bos taurus Reactome:REACT_1590 G1 Phase, Homo sapiens Reactome:REACT_29795 G1 Phase, Taeniopygia guttata Reactome:REACT_34060 G1 Phase, Canis familiaris Reactome:REACT_78665 G1 Phase, Gallus gallus Reactome:REACT_78866 G1 Phase, Sus scrofa Reactome:REACT_83686 G1 Phase, Danio rerio Reactome:REACT_91654 G1 Phase, Mus musculus Reactome:REACT_93384 G1 Phase, Rattus norvegicus Reactome:REACT_93574 G1 Phase, Xenopus tropicalis The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle. Reactome:REACT_105829 Reactome:REACT_108550 Reactome:REACT_110039 Reactome:REACT_28988 Reactome:REACT_32013 Reactome:REACT_34043 Reactome:REACT_78838 Reactome:REACT_78845 Reactome:REACT_81914 Reactome:REACT_82813 Reactome:REACT_85811 Reactome:REACT_89318 Reactome:REACT_899 Reactome:REACT_92500 Reactome:REACT_92759 Reactome:REACT_95174 Reactome:REACT_96081 Reactome:REACT_97603 Reactome:REACT_99645 S phase of mitotic cell cycle S-phase of mitotic cell cycle biological_process GO:0000084 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic S phase The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle. GOC:mtg_cell_cycle Reactome:REACT_105829 S Phase, Caenorhabditis elegans Reactome:REACT_108550 S Phase, Rattus norvegicus Reactome:REACT_110039 S Phase, Schizosaccharomyces pombe Reactome:REACT_28988 S Phase, Taeniopygia guttata Reactome:REACT_32013 S Phase, Mycobacterium tuberculosis Reactome:REACT_34043 S Phase, Oryza sativa Reactome:REACT_78838 S Phase, Plasmodium falciparum Reactome:REACT_78845 S Phase, Xenopus tropicalis Reactome:REACT_81914 S Phase, Saccharomyces cerevisiae Reactome:REACT_82813 S Phase, Arabidopsis thaliana Reactome:REACT_85811 S Phase, Sus scrofa Reactome:REACT_89318 S Phase, Drosophila melanogaster Reactome:REACT_899 S Phase, Homo sapiens Reactome:REACT_92500 S Phase, Mus musculus Reactome:REACT_92759 S Phase, Canis familiaris Reactome:REACT_95174 S Phase, Gallus gallus Reactome:REACT_96081 S Phase, Dictyostelium discoideum Reactome:REACT_97603 S Phase, Danio rerio Reactome:REACT_99645 S Phase, Bos taurus The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis. Reactome:REACT_105223 Reactome:REACT_105307 Reactome:REACT_106415 Reactome:REACT_106836 Reactome:REACT_1915 Reactome:REACT_28975 Reactome:REACT_85928 Reactome:REACT_96332 G2 phase of mitotic cell cycle biological_process GO:0000085 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic G2 phase The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis. GOC:mtg_cell_cycle Reactome:REACT_105223 G2 Phase, Mus musculus Reactome:REACT_105307 G2 Phase, Canis familiaris Reactome:REACT_106415 G2 Phase, Xenopus tropicalis Reactome:REACT_106836 G2 Phase, Bos taurus Reactome:REACT_1915 G2 Phase, Homo sapiens Reactome:REACT_28975 G2 Phase, Rattus norvegicus Reactome:REACT_85928 G2 Phase, Sus scrofa Reactome:REACT_96332 G2 Phase, Danio rerio The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex. Reactome:REACT_100942 Reactome:REACT_103766 Reactome:REACT_107882 Reactome:REACT_114616 Reactome:REACT_2203 Reactome:REACT_28929 Reactome:REACT_30388 Reactome:REACT_34062 Reactome:REACT_77778 Reactome:REACT_83880 Reactome:REACT_87036 Reactome:REACT_87230 Reactome:REACT_87807 Reactome:REACT_88018 Reactome:REACT_88369 Reactome:REACT_92702 mitotic G2/M transition biological_process GO:0000086 G2/M transition of mitotic cell cycle The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex. GOC:mtg_cell_cycle Reactome:REACT_100942 G2/M Transition, Danio rerio Reactome:REACT_103766 G2/M Transition, Schizosaccharomyces pombe Reactome:REACT_107882 G2/M Transition, Sus scrofa Reactome:REACT_114616 G2/M Transition, Arabidopsis thaliana Reactome:REACT_2203 G2/M Transition, Homo sapiens Reactome:REACT_28929 G2/M Transition, Xenopus tropicalis Reactome:REACT_30388 G2/M Transition, Gallus gallus Reactome:REACT_34062 G2/M Transition, Mus musculus Reactome:REACT_77778 G2/M Transition, Taeniopygia guttata Reactome:REACT_83880 G2/M Transition, Drosophila melanogaster Reactome:REACT_87036 G2/M Transition, Saccharomyces cerevisiae Reactome:REACT_87230 G2/M Transition, Canis familiaris Reactome:REACT_87807 G2/M Transition, Dictyostelium discoideum Reactome:REACT_88018 G2/M Transition, Caenorhabditis elegans Reactome:REACT_88369 G2/M Transition, Rattus norvegicus Reactome:REACT_92702 G2/M Transition, Bos taurus A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle. Reactome:REACT_105412 Reactome:REACT_107095 Reactome:REACT_109059 Reactome:REACT_29488 Reactome:REACT_33490 Reactome:REACT_82055 Reactome:REACT_87132 Reactome:REACT_88263 Reactome:REACT_910 Reactome:REACT_92998 Reactome:REACT_93131 Reactome:REACT_93566 Reactome:REACT_93720 Reactome:REACT_94536 M phase of mitotic cell cycle M-phase of mitotic cell cycle biological_process GO:0000087 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic M phase A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle. GOC:mtg_cell_cycle Reactome:REACT_105412 M Phase, Mus musculus Reactome:REACT_107095 M Phase, Dictyostelium discoideum Reactome:REACT_109059 M Phase, Saccharomyces cerevisiae Reactome:REACT_29488 M Phase, Canis familiaris Reactome:REACT_33490 M Phase, Caenorhabditis elegans Reactome:REACT_82055 M Phase, Rattus norvegicus Reactome:REACT_87132 M Phase, Bos taurus Reactome:REACT_88263 M Phase, Xenopus tropicalis Reactome:REACT_910 M Phase, Homo sapiens Reactome:REACT_92998 M Phase, Danio rerio Reactome:REACT_93131 M Phase, Schizosaccharomyces pombe Reactome:REACT_93566 M Phase, Gallus gallus Reactome:REACT_93720 M Phase, Drosophila melanogaster Reactome:REACT_94536 M Phase, Taeniopygia guttata The cell cycle phase which is the first stage of M phase of mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. Reactome:REACT_100605 Reactome:REACT_102122 Reactome:REACT_105127 Reactome:REACT_106058 Reactome:REACT_28443 Reactome:REACT_28607 Reactome:REACT_32677 Reactome:REACT_765 Reactome:REACT_79474 Reactome:REACT_80300 Reactome:REACT_83888 Reactome:REACT_90347 Reactome:REACT_90481 biological_process GO:0000088 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic prophase Reactome:REACT_100605 Mitotic Prophase, Saccharomyces cerevisiae Reactome:REACT_102122 Mitotic Prophase, Mus musculus Reactome:REACT_105127 Mitotic Prophase, Danio rerio Reactome:REACT_106058 Mitotic Prophase, Drosophila melanogaster Reactome:REACT_28443 Mitotic Prophase, Taeniopygia guttata Reactome:REACT_28607 Mitotic Prophase, Rattus norvegicus Reactome:REACT_32677 Mitotic Prophase, Xenopus tropicalis Reactome:REACT_765 Mitotic Prophase, Homo sapiens Reactome:REACT_79474 Mitotic Prophase, Caenorhabditis elegans Reactome:REACT_80300 Mitotic Prophase, Gallus gallus Reactome:REACT_83888 Mitotic Prophase, Dictyostelium discoideum Reactome:REACT_90347 Mitotic Prophase, Canis familiaris Reactome:REACT_90481 Mitotic Prophase, Schizosaccharomyces pombe The cell cycle phase which is the first stage of M phase of mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. GOC:mtg_cell_cycle The cell cycle phase, following prophase, during which chromosomes become aligned on the equatorial plate of the cell as part of a mitotic cell cycle. Reactome:REACT_434 biological_process GO:0000089 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic metaphase The cell cycle phase, following prophase, during which chromosomes become aligned on the equatorial plate of the cell as part of a mitotic cell cycle. GOC:mtg_cell_cycle Reactome:REACT_434 Mitotic Metaphase, Homo sapiens The cell cycle phase which follows anaphase during M phase of mitosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. biological_process GO:0000093 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic telophase The cell cycle phase which follows anaphase during M phase of mitosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. GOC:mtg_cell_cycle A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. microtubule cytoskeleton organisation microtubule dynamics biological_process microtubule cytoskeleton organization and biogenesis GO:0000226 microtubule cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. GOC:mah microtubule cytoskeleton organisation GOC:mah microtubule dynamics GOC:dph GOC:tb microtubule cytoskeleton organization and biogenesis GOC:mah The cell cycle phase in higher eukaryotes which follows mitotic prophase and during which the nuclear envelope is disrupted and breaks into membrane vesicles, and the spindle microtubules enter the nuclear region. Kinetochores mature on each centromere and attach to some of the spindle microtubules. Kinetochore microtubules begin the process of aligning chromosomes in one plane halfway between the poles. Reactome:REACT_102823 Reactome:REACT_104270 Reactome:REACT_105082 Reactome:REACT_114704 Reactome:REACT_118069 Reactome:REACT_118526 Reactome:REACT_118539 Reactome:REACT_31336 Reactome:REACT_31385 Reactome:REACT_682 Reactome:REACT_79351 Reactome:REACT_83126 Reactome:REACT_98905 Reactome:REACT_99376 biological_process GO:0000236 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic prometaphase The cell cycle phase in higher eukaryotes which follows mitotic prophase and during which the nuclear envelope is disrupted and breaks into membrane vesicles, and the spindle microtubules enter the nuclear region. Kinetochores mature on each centromere and attach to some of the spindle microtubules. Kinetochore microtubules begin the process of aligning chromosomes in one plane halfway between the poles. GOC:mtg_cell_cycle Reactome:REACT_102823 Mitotic Prometaphase, Mus musculus Reactome:REACT_104270 Mitotic Prometaphase, Bos taurus Reactome:REACT_105082 Mitotic Prometaphase, Dictyostelium discoideum Reactome:REACT_114704 Mitotic Prometaphase, Schizosaccharomyces pombe Reactome:REACT_118069 Mitotic Prometaphase, Gallus gallus Reactome:REACT_118526 Mitotic Prometaphase, Saccharomyces cerevisiae Reactome:REACT_118539 Mitotic Prometaphase, Taeniopygia guttata Reactome:REACT_31336 Mitotic Prometaphase, Danio rerio Reactome:REACT_31385 Mitotic Prometaphase, Caenorhabditis elegans Reactome:REACT_682 Mitotic Prometaphase, Homo sapiens Reactome:REACT_79351 Mitotic Prometaphase, Rattus norvegicus Reactome:REACT_83126 Mitotic Prometaphase, Drosophila melanogaster Reactome:REACT_98905 Mitotic Prometaphase, Xenopus tropicalis Reactome:REACT_99376 Mitotic Prometaphase, Canis familiaris Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. Reactome:REACT_100451 Reactome:REACT_104035 Reactome:REACT_104195 Reactome:REACT_105856 Reactome:REACT_108233 Reactome:REACT_152 Reactome:REACT_28464 Reactome:REACT_28953 Reactome:REACT_33388 Reactome:REACT_53493 Reactome:REACT_79085 Reactome:REACT_84794 Reactome:REACT_85137 Reactome:REACT_85950 Reactome:REACT_90332 Reactome:REACT_90846 Reactome:REACT_96281 Reactome:REACT_97744 Reactome:REACT_98208 biological_process GO:0000278 mitotic cell cycle Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 Reactome:69278 Reactome:REACT_100451 Cell Cycle, Mitotic, Taeniopygia guttata Reactome:REACT_104035 Cell Cycle, Mitotic, Sus scrofa Reactome:REACT_104195 Cell Cycle, Mitotic, Canis familiaris Reactome:REACT_105856 Cell Cycle, Mitotic, Danio rerio Reactome:REACT_108233 Cell Cycle, Mitotic, Saccharomyces cerevisiae Reactome:REACT_152 Cell Cycle, Mitotic, Homo sapiens Reactome:REACT_28464 Cell Cycle, Mitotic, Xenopus tropicalis Reactome:REACT_28953 Cell Cycle, Mitotic, Bos taurus Reactome:REACT_33388 Cell Cycle, Mitotic, Rattus norvegicus Reactome:REACT_53493 Cell Cycle, Mitotic, Plasmodium falciparum Reactome:REACT_79085 Cell Cycle, Mitotic, Schizosaccharomyces pombe Reactome:REACT_84794 Cell Cycle, Mitotic, Caenorhabditis elegans Reactome:REACT_85137 Cell Cycle, Mitotic, Gallus gallus Reactome:REACT_85950 Cell Cycle, Mitotic, Arabidopsis thaliana Reactome:REACT_90332 Cell Cycle, Mitotic, Mus musculus Reactome:REACT_90846 Cell Cycle, Mitotic, Oryza sativa Reactome:REACT_96281 Cell Cycle, Mitotic, Drosophila melanogaster Reactome:REACT_97744 Cell Cycle, Mitotic, Dictyostelium discoideum Reactome:REACT_98208 Cell Cycle, Mitotic, Mycobacterium tuberculosis A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase. Wikipedia:M_phase M-phase biological_process GO:0000279 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). M phase A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase. GOC:mtg_cell_cycle The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. biological_process karyokinesis GO:0000280 nuclear division The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. GOC:mah The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides. DNA breakdown, endonucleolytic DNA degradation, endonucleolytic endonucleolytic DNA catabolism endonucleolytic degradation of DNA biological_process GO:0000737 DNA catabolic process, endonucleolytic The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides. GOC:elh GOC:mah The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome. GO:0097521 centromere complex chromosome, centric region cellular_component centromere chromosome, pericentric region GO:0000775 Note that this term can be used in place of the obsolete cellular component term 'centromere ; GO:0005698'. chromosome, centromeric region The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome. GOC:cjm GOC:elh GOC:kmv GOC:pr A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules. GO:0005699 Wikipedia:Kinetochore cellular_component GO:0000776 Note that the kinetochore overlaps the centromeric DNA, but centromeric DNA is not part of the kinetochore. kinetochore A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules. GOC:elh The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets. biological_process GO:0000819 sister chromatid segregation The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets. GOC:ai GOC:elh The developmental process in which the size or shape of a cell is generated and organized. GO:0007148 GO:0045790 GO:0045791 cellular morphogenesis biological_process GO:0000902 cell morphogenesis The developmental process in which the size or shape of a cell is generated and organized. GOC:clt GOC:dph GOC:go_curators GOC:tb The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. biological_process GO:0000904 cell morphogenesis involved in differentiation The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. GOC:go_curators The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells. GO:0007104 GO:0016288 GO:0033205 Reactome:REACT_101918 Reactome:REACT_108805 Reactome:REACT_1932 Reactome:REACT_30667 Reactome:REACT_32636 Reactome:REACT_78494 Reactome:REACT_84722 Reactome:REACT_87726 Reactome:REACT_92849 Reactome:REACT_93374 Reactome:REACT_94382 Reactome:REACT_98952 Reactome:REACT_99118 Wikipedia:Cytokinesis cell cycle cytokinesis cytokinesis involved in cell cycle biological_process GO:0000910 Note that when annotating eukaryotic species, mitotic or meiotic cytokinesis should always be specified for manual annotation and for prokaryotic species use 'FtsZ-dependent cytokinesis ; GO:0043093' or Cdv-dependent cytokinesis ; GO:0061639. Also, note that cytokinesis does not necessarily result in physical separation and detachment of the two daughter cells from each other. cytokinesis The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells. GOC:mtg_cell_cycle Reactome:REACT_101918 Mitotic Telophase /Cytokinesis, Mus musculus Reactome:REACT_108805 Mitotic Telophase /Cytokinesis, Dictyostelium discoideum Reactome:REACT_1932 Mitotic Telophase /Cytokinesis, Homo sapiens Reactome:REACT_30667 Mitotic Telophase /Cytokinesis, Schizosaccharomyces pombe Reactome:REACT_32636 Mitotic Telophase /Cytokinesis, Bos taurus Reactome:REACT_78494 Mitotic Telophase /Cytokinesis, Danio rerio Reactome:REACT_84722 Mitotic Telophase /Cytokinesis, Gallus gallus Reactome:REACT_87726 Mitotic Telophase /Cytokinesis, Xenopus tropicalis Reactome:REACT_92849 Mitotic Telophase /Cytokinesis, Taeniopygia guttata Reactome:REACT_93374 Mitotic Telophase /Cytokinesis, Canis familiaris Reactome:REACT_94382 Mitotic Telophase /Cytokinesis, Drosophila melanogaster Reactome:REACT_98952 Mitotic Telophase /Cytokinesis, Rattus norvegicus Reactome:REACT_99118 Mitotic Telophase /Cytokinesis, Caenorhabditis elegans cytokinesis involved in cell cycle GOC:dph GOC:tb Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair. kchris 2010-08-10T10:56:24Z molecular_function GO:0000975 regulatory region DNA binding Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair. GOC:txnOH Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. kchris 2010-08-10T11:00:02Z molecular_function GO:0000976 The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". transcription regulatory region sequence-specific DNA binding Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. GOC:txnOH Interacting selectively and non-covalently with a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair. kchris 2010-10-21T04:08:56Z molecular_function GO:0001067 regulatory region nucleic acid binding Interacting selectively and non-covalently with a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair. GOC:txnOH Interacting selectively and non-covalently with a DNA or RNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. kchris 2010-10-21T04:37:54Z transcription factor activity molecular_function GO:0001071 Note that this term is in the subset of terms that should not be used for direct gene product annotation. This term does not provide specificity with respect to the type of nucleic acid binding, e.g. RNA or DNA. Please use a child term that provides that specificity or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. nucleic acid binding transcription factor activity Interacting selectively and non-covalently with a DNA or RNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. GOC:txnOH A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber. stress fibre cellular_component actin cable GO:0001725 stress fiber A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber. PMID:16651381 actin cable GOC:mah Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. biological_process necrosis GO:0001906 cell killing Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. GOC:add The directed killing of a target cell by a leukocyte. immune cell mediated cell death immune cell mediated cell killing immune cell mediated cytotoxicity leucocyte mediated cytotoxicity biological_process GO:0001909 This term was improved by GO_REF:0000022. It was moved. Note that this term and its children describe contact-dependent killing of target cells by lymphocytes and myeloid cells of the immune system. leukocyte mediated cytotoxicity The directed killing of a target cell by a leukocyte. GOC:add GOC:mtg_15nov05 GO_REF:0000022 ISBN:0781735149 PMID:11911826 The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. T cell mediated apoptosis T cell mediated cell death T cell mediated cell killing T lymphocyte mediated cytotoxicity T-cell mediated apoptosis T-cell mediated cell death T-cell mediated cell killing T-cell mediated cytotoxicity T-lymphocyte mediated cytotoxicity biological_process T cell mediated cytolysis GO:0001913 Note that either or both mechanisms mentioned in the definition may be used in this process. Note that both granule release and the engagement of death receptors on target cells result in the induction of apoptosis in the target cell. Note that both CD4 and CD8 positive T cells can mediate apoptosis of target cells, independently of their definition as 'helper' T cells or not. T cell mediated cytotoxicity The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. GOC:add GOC:pr ISBN:0781735149 PMID:11911826 An actin-rich adhesion structure characterized by formation upon cell substrate contact and localization at the substrate-attached part of the cell, contain an F-actin-rich core surrounded by a ring structure containing proteins such as vinculin and talin, and have a diameter of 0.5 mm. Wikipedia:Podosome cellular_component GO:0002102 Note that podosomes can be distinguished from other F-actin-rich structures or from other matrix contacts. For example, focal adhesions and focal contacts do not display a core structure of F-actin. Unlike focal adhesions, podosome assembly does not require de novo protein synthesis. However, most of the podosome ring components are found in focal adhesions and other cell-matrix contacts. Podosomes are typically found in cells that cross tissue boundaries, recruited to the leading edge of migrating cells, and are often sites of extracellular matrix degradation. podosome An actin-rich adhesion structure characterized by formation upon cell substrate contact and localization at the substrate-attached part of the cell, contain an F-actin-rich core surrounded by a ring structure containing proteins such as vinculin and talin, and have a diameter of 0.5 mm. PMID:12837608 PMID:15890982 An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory). Wikipedia:Adaptive_immune_system acquired immune response biological_process GO:0002250 This term was added by GO_REF:0000022. adaptive immune response An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory). GOC:add GOC:mtg_15nov05 GO_REF:0000022 ISBN:0781735149 acquired immune response ISBN:068340007X Any process of the immune system that can potentially contribute to an immune response. biological_process GO:0002252 This term was added by GO_REF:0000022. immune effector process Any process of the immune system that can potentially contribute to an immune response. GOC:add GOC:mtg_15nov05 GO_REF:0000022 ISBN:0781735149 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a tumor cell. biological_process GO:0002347 response to tumor cell Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a tumor cell. GOC:add ISBN:0781735149 PMID:16730260 Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. Wikipedia:Immune_system biological_process GO:0002376 Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022. immune system process Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. GOC:add GOC:mtg_15nov05 GO_REF:0000022 An immune system process that functions in the response of an organism to a tumor cell. biological_process GO:0002418 immune response to tumor cell An immune system process that functions in the response of an organism to a tumor cell. GOC:add ISBN:0781735149 PMID:16730260 The directed killing of a tumor cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. T lymphocyte mediated cytotoxicity directed against tumor cell target T-cell mediated cytotoxicity directed against tumor cell target T-lymphocyte mediated cytotoxicity directed against tumor cell target biological_process GO:0002419 Note that either or both mechanisms mentioned in the definition may be used in this process. Note that both granule release and the engagement of death receptors on target cells result in induction of apoptosis in the target cell. T cell mediated cytotoxicity directed against tumor cell target The directed killing of a tumor cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. GOC:add ISBN:0781735149 PMID:16730260 An immune response mediated by a T cell triggered in response to the presence of a tumor cell. biological_process GO:0002424 Note that this term includes tolerogenic responses to tumor cells mediated by responding T cells. T cell mediated immune response to tumor cell An immune response mediated by a T cell triggered in response to the presence of a tumor cell. GOC:add ISBN:0781735149 PMID:16730260 Any process involved in the carrying out of an immune response by a leukocyte. GO:0019723 GO:0042087 immune cell effector process immune cell mediated immunity leucocyte immune effector process leucocyte mediated immunity leukocyte immune effector process biological_process cell-mediated immune response cellular immune response GO:0002443 This term was added by GO_REF:0000022. leukocyte mediated immunity Any process involved in the carrying out of an immune response by a leukocyte. GOC:add GOC:mtg_15nov05 GO_REF:0000022 ISBN:0781735149 Any process involved in the carrying out of an immune response by a lymphocyte. cell-mediated immunity cellular immune response biological_process GO:0002449 This term was added by GO_REF:0000022. lymphocyte mediated immunity Any process involved in the carrying out of an immune response by a lymphocyte. GOC:add GOC:mtg_15nov05 GO_REF:0000022 ISBN:0781735149 Any process involved in the carrying out of an immune response by a T cell. cell-mediated immunity cellular immune response T lymphocyte mediated immunity T-cell mediated immunity T-lymphocyte mediated immunity biological_process GO:0002456 This term was added by GO_REF:0000022. T cell mediated immunity Any process involved in the carrying out of an immune response by a T cell. GOC:add GOC:mtg_15nov05 GO_REF:0000022 ISBN:0781735149 An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains, and allowing for enhanced responses upon subsequent exposures to the same antigen (immunological memory). Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies). An example of this is the adaptive immune response found in Mus musculus. biological_process GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains, and allowing for enhanced responses upon subsequent exposures to the same antigen (immunological memory). Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies). An example of this is the adaptive immune response found in Mus musculus. GOC:add GOC:mtg_sensu ISBN:0781735149 Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. GO:0005554 molecular function molecular_function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. molecular_function Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. GOC:go_curators Interacting selectively and non-covalently with any nucleic acid. molecular_function GO:0003676 nucleic acid binding Interacting selectively and non-covalently with any nucleic acid. GOC:jl Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). plasmid binding molecular_function microtubule/chromatin interaction GO:0003677 DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GOC:dph GOC:jl GOC:tb GOC:vw Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. GO:0000130 transcription factor activity molecular_function GO:0003700 sequence-specific DNA binding transcription factor activity Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. GOC:curators GOC:txnOH Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence. EC:2.7.7.- Reactome:REACT_104705 Reactome:REACT_106476 Reactome:REACT_108407 Reactome:REACT_109443 Reactome:REACT_113385 Reactome:REACT_114466 Reactome:REACT_115824 Reactome:REACT_116122 Reactome:REACT_28249 Reactome:REACT_30494 Reactome:REACT_30995 Reactome:REACT_31549 Reactome:REACT_33436 Reactome:REACT_77280 Reactome:REACT_7985 Reactome:REACT_8019 Reactome:REACT_80834 Reactome:REACT_81691 Reactome:REACT_83982 Reactome:REACT_85286 Reactome:REACT_86666 Reactome:REACT_90823 Reactome:REACT_93232 Reactome:REACT_94534 Reactome:REACT_94768 Reactome:REACT_95176 Reactome:REACT_96912 Reactome:REACT_97770 molecular_function GO:0003720 telomerase activity Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence. GOC:krc Reactome:REACT_104705 Elongation of Extended Telomeric Chromosome End, Saccharomyces cerevisiae Reactome:REACT_106476 Elongation Of The Telomeric Chromosome End, Bos taurus Reactome:REACT_108407 Elongation of Extended Telomeric Chromosome End, Oryza sativa Reactome:REACT_109443 Elongation Of The Telomeric Chromosome End, Danio rerio Reactome:REACT_113385 Elongation Of The Telomeric Chromosome End, Xenopus tropicalis Reactome:REACT_114466 Elongation of Extended Telomeric Chromosome End, Xenopus tropicalis Reactome:REACT_115824 Elongation and translocation of the extended telomeric chromosome end, Gallus gallus Reactome:REACT_116122 Elongation and translocation of the telomeric chromosome end, Gallus gallus Reactome:REACT_28249 Elongation of Extended Telomeric Chromosome End, Gallus gallus Reactome:REACT_30494 Elongation Of The Telomeric Chromosome End, Sus scrofa Reactome:REACT_30995 Elongation Of The Telomeric Chromosome End, Canis familiaris Reactome:REACT_31549 Elongation Of The Telomeric Chromosome End, Saccharomyces cerevisiae Reactome:REACT_33436 Elongation of Extended Telomeric Chromosome End, Danio rerio Reactome:REACT_77280 Elongation of Extended Telomeric Chromosome End, Arabidopsis thaliana Reactome:REACT_7985 Elongation of Extended Telomeric Chromosome End, Homo sapiens Reactome:REACT_8019 Elongation Of The Telomeric Chromosome End, Homo sapiens Reactome:REACT_80834 Elongation Of The Telomeric Chromosome End, Mus musculus Reactome:REACT_81691 Elongation of Extended Telomeric Chromosome End, Canis familiaris Reactome:REACT_83982 Elongation Of The Telomeric Chromosome End, Oryza sativa Reactome:REACT_85286 Elongation of Extended Telomeric Chromosome End, Bos taurus Reactome:REACT_86666 Elongation of Extended Telomeric Chromosome End, Sus scrofa Reactome:REACT_90823 Elongation of Extended Telomeric Chromosome End, Mus musculus Reactome:REACT_93232 Elongation Of The Telomeric Chromosome End, Schizosaccharomyces pombe Reactome:REACT_94534 Elongation Of The Telomeric Chromosome End, Taeniopygia guttata Reactome:REACT_94768 Elongation of Extended Telomeric Chromosome End, Schizosaccharomyces pombe Reactome:REACT_95176 Elongation Of The Telomeric Chromosome End, Gallus gallus Reactome:REACT_96912 Elongation of Extended Telomeric Chromosome End, Taeniopygia guttata Reactome:REACT_97770 Elongation Of The Telomeric Chromosome End, Arabidopsis thaliana Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. Wikipedia:Enzyme enzyme activity molecular_function GO:0003824 catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. ISBN:0198506732 enzyme activity GOC:dph GOC:tb Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. EC:2.7.7.49 MetaCyc:RNA-DIRECTED-DNA-POLYMERASE-RXN Reactome:REACT_9039 Reactome:REACT_9049 DNA nucleotidyltransferase (RNA-directed) activity RNA revertase activity RNA-dependent DNA polymerase activity RNA-dependent deoxyribonucleate nucleotidyltransferase activity RNA-instructed DNA polymerase activity deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) activity reverse transcriptase activity RNA-directed DNA polymerase, group II intron encoded RNA-directed DNA polymerase, transposon encoded molecular_function RT revertase activity GO:0003964 RNA-directed DNA polymerase activity Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. EC:2.7.7.49 Reactome:REACT_9039 Synthesis of minus strand strong stop DNA (-sssDNA), Homo sapiens Reactome:REACT_9049 Minus strand DNA synthesis resumes, Homo sapiens DNA nucleotidyltransferase (RNA-directed) activity EC:2.7.7.49 RNA revertase activity EC:2.7.7.49 RNA-dependent DNA polymerase activity EC:2.7.7.49 RNA-dependent deoxyribonucleate nucleotidyltransferase activity EC:2.7.7.49 RNA-instructed DNA polymerase activity EC:2.7.7.49 deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) activity EC:2.7.7.49 reverse transcriptase activity EC:2.7.7.49 RT EC:2.7.7.49 revertase activity EC:2.7.7.49 Catalysis of the hydrolysis of ester linkages within nucleic acids. EC:3.1.-.- molecular_function GO:0004518 Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. nuclease activity Catalysis of the hydrolysis of ester linkages within nucleic acids. ISBN:0198547684 Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks. Reactome:REACT_100654 Reactome:REACT_101397 Reactome:REACT_103600 Reactome:REACT_106502 Reactome:REACT_108614 Reactome:REACT_110731 Reactome:REACT_112366 Reactome:REACT_1124 Reactome:REACT_112509 Reactome:REACT_112615 Reactome:REACT_112782 Reactome:REACT_113127 Reactome:REACT_113480 Reactome:REACT_113819 Reactome:REACT_114931 Reactome:REACT_115221 Reactome:REACT_115226 Reactome:REACT_115382 Reactome:REACT_115937 Reactome:REACT_116011 Reactome:REACT_1914 Reactome:REACT_34610 Reactome:REACT_6746 Reactome:REACT_6774 Reactome:REACT_77706 Reactome:REACT_78624 Reactome:REACT_79198 Reactome:REACT_80387 Reactome:REACT_80628 Reactome:REACT_80681 Reactome:REACT_80797 Reactome:REACT_81714 Reactome:REACT_87541 Reactome:REACT_89800 Reactome:REACT_90034 Reactome:REACT_90935 Reactome:REACT_92894 molecular_function GO:0004519 endonuclease activity Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks. GOC:mah ISBN:0198547684 Reactome:REACT_100654 3'- incision of DNA by XPG in GG-NER, Arabidopsis thaliana Reactome:REACT_101397 3'- incision of DNA by XPG in GG-NER, Danio rerio Reactome:REACT_103600 3'- incision of DNA by XPG in GG-NER, Gallus gallus Reactome:REACT_106502 3'- incision of DNA by XPG in GG-NER, Rattus norvegicus Reactome:REACT_108614 3'- incision of DNA by XPG in GG-NER, Taeniopygia guttata Reactome:REACT_110731 3'- incision of DNA by XPG in GG-NER, Xenopus tropicalis Reactome:REACT_112366 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Danio rerio Reactome:REACT_1124 3'- incision of DNA by XPG in GG-NER, Homo sapiens Reactome:REACT_112509 Cleavage of mRNA at the 3'-end, Arabidopsis thaliana Reactome:REACT_112615 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Rattus norvegicus Reactome:REACT_112782 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Xenopus tropicalis Reactome:REACT_113127 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Taeniopygia guttata Reactome:REACT_113480 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Gallus gallus Reactome:REACT_113819 Cleavage of mRNA at the 3'-end, Drosophila melanogaster Reactome:REACT_114931 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Canis familiaris Reactome:REACT_115221 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Mus musculus Reactome:REACT_115226 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Bos taurus Reactome:REACT_115382 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Sus scrofa Reactome:REACT_115937 Displacement of DNA glycosylase and endonucleolytic cleavage by DNA-lyase, Gallus gallus Reactome:REACT_116011 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Gallus gallus Reactome:REACT_1914 Cleavage of mRNA at the 3'-end, Homo sapiens Reactome:REACT_34610 Cleavage of mRNA at the 3'-end, Bos taurus Reactome:REACT_6746 Removal of 3'-phosphate moiety from DSB ends, Homo sapiens Reactome:REACT_6774 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Homo sapiens Reactome:REACT_77706 Cleavage of mRNA at the 3'-end, Taeniopygia guttata Reactome:REACT_78624 3'- incision of DNA by XPG in GG-NER, Canis familiaris Reactome:REACT_79198 Cleavage of mRNA at the 3'-end, Canis familiaris Reactome:REACT_80387 3'- incision of DNA by XPG in GG-NER, Caenorhabditis elegans Reactome:REACT_80628 3'- incision of DNA by XPG in GG-NER, Saccharomyces cerevisiae Reactome:REACT_80681 3'- incision of DNA by XPG in GG-NER, Bos taurus Reactome:REACT_80797 Cleavage of mRNA at the 3'-end, Mus musculus Reactome:REACT_81714 3'- incision of DNA by XPG in GG-NER, Oryza sativa Reactome:REACT_87541 Cleavage of mRNA at the 3'-end, Xenopus tropicalis Reactome:REACT_89800 3'- incision of DNA by XPG in GG-NER, Schizosaccharomyces pombe Reactome:REACT_90034 3'- incision of DNA by XPG in GG-NER, Mus musculus Reactome:REACT_90935 3'- incision of DNA by XPG in GG-NER, Sus scrofa Reactome:REACT_92894 3'- incision of DNA by XPG in GG-NER, Drosophila melanogaster Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks. Reactome:REACT_101184 Reactome:REACT_101250 Reactome:REACT_101987 Reactome:REACT_103441 Reactome:REACT_103771 Reactome:REACT_104010 Reactome:REACT_104673 Reactome:REACT_104703 Reactome:REACT_104968 Reactome:REACT_106756 Reactome:REACT_109040 Reactome:REACT_109537 Reactome:REACT_109692 Reactome:REACT_110386 Reactome:REACT_112122 Reactome:REACT_112152 Reactome:REACT_115154 Reactome:REACT_115463 Reactome:REACT_115479 Reactome:REACT_1274 Reactome:REACT_1311 Reactome:REACT_1964 Reactome:REACT_27164 Reactome:REACT_27209 Reactome:REACT_28610 Reactome:REACT_28960 Reactome:REACT_30718 Reactome:REACT_31162 Reactome:REACT_31548 Reactome:REACT_31660 Reactome:REACT_31823 Reactome:REACT_32833 Reactome:REACT_33043 Reactome:REACT_78421 Reactome:REACT_79265 Reactome:REACT_80173 Reactome:REACT_80298 Reactome:REACT_80967 Reactome:REACT_811 Reactome:REACT_81197 Reactome:REACT_82925 Reactome:REACT_83838 Reactome:REACT_85019 Reactome:REACT_88339 Reactome:REACT_90087 Reactome:REACT_92741 Reactome:REACT_94592 Reactome:REACT_94820 Reactome:REACT_95903 Reactome:REACT_97114 Reactome:REACT_98405 Reactome:REACT_98417 Reactome:REACT_99783 molecular_function DNA nicking activity endonuclease G activity GO:0004520 endodeoxyribonuclease activity Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks. GOC:mah ISBN:0198547684 Reactome:REACT_101184 5'-incision of DNA by ERCC1-XPF in GG-NER, Danio rerio Reactome:REACT_101250 5' incision leading to excision of DNA fragment with lesion in TC-NER, Caenorhabditis elegans Reactome:REACT_101987 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Dictyostelium discoideum Reactome:REACT_103441 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Rattus norvegicus Reactome:REACT_103771 3' incision of the lesioned strand of DNA in TC-NER, Xenopus tropicalis Reactome:REACT_104010 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Danio rerio Reactome:REACT_104673 5' incision leading to excision of DNA fragment with lesion in TC-NER, Schizosaccharomyces pombe Reactome:REACT_104703 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Taeniopygia guttata Reactome:REACT_104968 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Sus scrofa Reactome:REACT_106756 3' incision of the lesioned strand of DNA in TC-NER, Drosophila melanogaster Reactome:REACT_109040 3' incision of the lesioned strand of DNA in TC-NER, Canis familiaris Reactome:REACT_109537 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Xenopus tropicalis Reactome:REACT_109692 3' incision of the lesioned strand of DNA in TC-NER, Sus scrofa Reactome:REACT_110386 3' incision of the lesioned strand of DNA in TC-NER, Danio rerio Reactome:REACT_112122 5'-incision of DNA by ERCC1-XPF in GG-NER, Xenopus tropicalis Reactome:REACT_112152 3' incision of the lesioned strand of DNA in TC-NER, Taeniopygia guttata Reactome:REACT_115154 5' incision leading to excision of DNA fragment with lesion in TC-NER, Gallus gallus Reactome:REACT_115463 5' incision leading to excision of DNA fragment with lesion in TC-NER, Taeniopygia guttata Reactome:REACT_115479 3' incision of the lesioned strand of DNA in TC-NER, Gallus gallus Reactome:REACT_1274 3' incision of the lesioned strand of DNA in TC-NER, Homo sapiens Reactome:REACT_1311 5'-incision of DNA by ERCC1-XPF in GG-NER, Homo sapiens Reactome:REACT_1964 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Homo sapiens Reactome:REACT_27164 Removal of SPO11 and Resection of 5' Ends of DNA (yeast), Saccharomyces cerevisiae Reactome:REACT_27209 Removal of SPO11 and Resection of 5' Ends of DNA, Homo sapiens Reactome:REACT_28610 5' incision leading to excision of DNA fragment with lesion in TC-NER, Bos taurus Reactome:REACT_28960 3' incision of the lesioned strand of DNA in TC-NER, Rattus norvegicus Reactome:REACT_30718 3' incision of the lesioned strand of DNA in TC-NER, Dictyostelium discoideum Reactome:REACT_31162 5' incision leading to excision of DNA fragment with lesion in TC-NER, Arabidopsis thaliana Reactome:REACT_31548 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Caenorhabditis elegans Reactome:REACT_31660 3' incision of the lesioned strand of DNA in TC-NER, Schizosaccharomyces pombe Reactome:REACT_31823 5' incision leading to excision of DNA fragment with lesion in TC-NER, Oryza sativa Reactome:REACT_32833 3' incision of the lesioned strand of DNA in TC-NER, Saccharomyces cerevisiae Reactome:REACT_33043 3' incision of the lesioned strand of DNA in TC-NER, Bos taurus Reactome:REACT_78421 5' incision leading to excision of DNA fragment with lesion in TC-NER, Sus scrofa Reactome:REACT_79265 5' incision leading to excision of DNA fragment with lesion in TC-NER, Dictyostelium discoideum Reactome:REACT_80173 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Mus musculus Reactome:REACT_80298 3' incision of the lesioned strand of DNA in TC-NER, Caenorhabditis elegans Reactome:REACT_80967 3' incision of the lesioned strand of DNA in TC-NER, Oryza sativa Reactome:REACT_811 5' incision leading to excision of DNA fragment with lesion in TC-NER, Homo sapiens Reactome:REACT_81197 5' incision leading to excision of DNA fragment with lesion in TC-NER, Mus musculus Reactome:REACT_82925 5' incision leading to excision of DNA fragment with lesion in TC-NER, Canis familiaris Reactome:REACT_83838 5'-incision of DNA by ERCC1-XPF in GG-NER, Rattus norvegicus Reactome:REACT_85019 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Drosophila melanogaster Reactome:REACT_88339 5' incision leading to excision of DNA fragment with lesion in TC-NER, Rattus norvegicus Reactome:REACT_90087 5' incision leading to excision of DNA fragment with lesion in TC-NER, Danio rerio Reactome:REACT_92741 3' incision of the lesioned strand of DNA in TC-NER, Arabidopsis thaliana Reactome:REACT_94592 5' incision leading to excision of DNA fragment with lesion in TC-NER, Drosophila melanogaster Reactome:REACT_94820 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Canis familiaris Reactome:REACT_95903 5'-incision of DNA by ERCC1-XPF in GG-NER, Mus musculus Reactome:REACT_97114 5' incision leading to excision of DNA fragment with lesion in TC-NER, Xenopus tropicalis Reactome:REACT_98405 5' incision leading to excision of DNA fragment with lesion in TC-NER, Saccharomyces cerevisiae Reactome:REACT_98417 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Bos taurus Reactome:REACT_99783 3' incision of the lesioned strand of DNA in TC-NER, Mus musculus DNA nicking activity GOC:mah Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid. GO:0004537 Reactome:REACT_100642 Reactome:REACT_101208 Reactome:REACT_110575 Reactome:REACT_13702 Reactome:REACT_29722 Reactome:REACT_31853 Reactome:REACT_90424 Reactome:REACT_95359 Reactome:REACT_98682 caspase-activated deoxyribonuclease activity molecular_function GO:0004536 deoxyribonuclease activity Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid. GOC:mah ISBN:0198547684 Reactome:REACT_100642 Cleavage of DNA by DFF40, Xenopus tropicalis Reactome:REACT_101208 Cleavage of DNA by DFF40, Bos taurus Reactome:REACT_110575 Cleavage of DNA by DFF40, Sus scrofa Reactome:REACT_13702 Cleavage of DNA by DFF40, Homo sapiens Reactome:REACT_29722 Cleavage of DNA by DFF40, Danio rerio Reactome:REACT_31853 Cleavage of DNA by DFF40, Taeniopygia guttata Reactome:REACT_90424 Cleavage of DNA by DFF40, Gallus gallus Reactome:REACT_95359 Cleavage of DNA by DFF40, Rattus norvegicus Reactome:REACT_98682 Cleavage of DNA by DFF40, Canis familiaris The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. Wikipedia:Binding_(molecular) ligand molecular_function GO:0005488 Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. binding The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. GOC:ceb GOC:mah ISBN:0198506732 The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. GO:0008372 NIF_Subcellular:sao-1337158144 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. cellular_component The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. GOC:go_curators NIF_Subcellular:sao-1337158144 subcellular entity NIF_Subcellular:nlx_subcell_100315 The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. Wikipedia:Intracellular internal to cell protoplasm cellular_component nucleocytoplasm protoplast GO:0005622 intracellular The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. ISBN:0198506732 nucleocytoplasm GOC:mah protoplast GOC:mah The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. cell and encapsulating structures NIF_Subcellular:sao1813327414 Wikipedia:Cell_(biology) cellular_component GO:0005623 cell The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:go_curators A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus cellular_component GO:0005634 nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. GOC:go_curators That part of the nuclear content other than the chromosomes or the nucleolus. NIF_Subcellular:sao661522542 Wikipedia:Nucleoplasm cellular_component GO:0005654 nucleoplasm That part of the nuclear content other than the chromosomes or the nucleolus. GOC:ma ISBN:0124325653 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. Wikipedia:Chromosome interphase chromosome prophase chromosome cellular_component chromatid GO:0005694 Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromosome A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. ISBN:0198547684 A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. NIF_Subcellular:sao1820400233 Wikipedia:Nucleolus cellular_component GO:0005730 nucleolus A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. ISBN:0198506732 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. Wikipedia:Cytoplasm cellular_component GO:0005737 cytoplasm All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. ISBN:0198547684 A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. NIF_Subcellular:sao1860313010 Wikipedia:Mitochondrion mitochondria cellular_component GO:0005739 Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.) mitochondrion A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. GOC:giardia ISBN:0198506732 A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. Wikipedia:Vacuole cellular_component vacuolar carboxypeptidase Y GO:0005773 vacuole A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. GOC:mtg_sensu ISBN:0198506732 The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). NIF_Subcellular:sao1036339110 Wikipedia:Endoplasmic_reticulum ER cellular_component GO:0005783 endoplasmic reticulum The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). ISBN:0198506732 A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. Golgi NIF_Subcellular:sao451912436 Wikipedia:Golgi_apparatus Golgi complex Golgi ribbon cellular_component GO:0005794 Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. Golgi apparatus A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. ISBN:0198506732 The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart. Wikipedia:Spindle_apparatus cellular_component GO:0005819 spindle The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart. ISBN:0198547684 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. NIF_Subcellular:sao101633890 Wikipedia:Cytosol cellular_component GO:0005829 cytosol The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GOC:hgd GOC:jl Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. Wikipedia:Cytoskeleton cellular_component GO:0005856 cytoskeleton Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. GOC:mah ISBN:0198547684 PMID:16959967 Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. NIF_Subcellular:sao1846835077 Wikipedia:Microtubule microtubuli microtubulus neurotubule cellular_component GO:0005874 microtubule Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. ISBN:0879693568 neurotubule NIF_Subcellular:sao248349196 Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole. cellular_component GO:0005876 spindle microtubule Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole. ISBN:0815316194 Any microtubule in the cytoplasm of a cell. non-spindle-associated astral microtubule cellular_component GO:0005881 cytoplasmic microtubule Any microtubule in the cytoplasm of a cell. GOC:mah A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. FMA:63850 NIF_Subcellular:sao1588493326 Wikipedia:Actin microfilament cellular_component GO:0005884 actin filament A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. GOC:mah ISBN:0198506732 PMID:10666339 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane cell membrane cellular membrane cytoplasmic membrane plasmalemma bacterial inner membrane inner endospore membrane plasma membrane lipid bilayer cellular_component GO:0005886 plasma membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. ISBN:0716731363 cellular membrane NIF_Subcellular:sao6433132645 plasma membrane lipid bilayer GOC:mah A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments. Wikipedia:Adherens_junction cellular_component GO:0005912 adherens junction A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments. GOC:mah ISBN:0198506732 http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html An adherens junction which connects a cell to the extracellular matrix. cellular_component hemi-adherens junction GO:0005924 cell-substrate adherens junction An adherens junction which connects a cell to the extracellular matrix. GOC:hb Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. GO:0008357 Wikipedia:Focal_adhesion focal contact cellular_component adhesion plaque hemi-adherens junction GO:0005925 focal adhesion Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. ISBN:0124325653 ISBN:0815316208 adhesion plaque PMID:3332661 A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. FMA:67181 NIF_Subcellular:sao787716553 Wikipedia:Cilium eukaryotic flagellum microtubule-based flagellum cellular_component flagellum GO:0005929 Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. cilium A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GOC:cilia GOC:kmv GOC:vw ISBN:0198547684 The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. Wikipedia:Cell_cortex cellular_component cell periphery peripheral cytoplasm GO:0005938 cell cortex The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. GOC:mah ISBN:0815316194 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GO:0055134 cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process nucleobase, nucleoside and nucleotide metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0006139 nucleobase-containing compound metabolic process Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:ai nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. GO:0055132 DNA metabolism cellular DNA metabolism biological_process GO:0006259 DNA metabolic process Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. ISBN:0198506732 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. GO:0055133 Reactome:REACT_100559 Reactome:REACT_101280 Reactome:REACT_101497 Reactome:REACT_102679 Reactome:REACT_103614 Reactome:REACT_104547 Reactome:REACT_105292 Reactome:REACT_105467 Reactome:REACT_105835 Reactome:REACT_106018 Reactome:REACT_106104 Reactome:REACT_106382 Reactome:REACT_106434 Reactome:REACT_106732 Reactome:REACT_107075 Reactome:REACT_107423 Reactome:REACT_108461 Reactome:REACT_108634 Reactome:REACT_108739 Reactome:REACT_108768 Reactome:REACT_108929 Reactome:REACT_109137 Reactome:REACT_112472 Reactome:REACT_113703 Reactome:REACT_29423 Reactome:REACT_29444 Reactome:REACT_29691 Reactome:REACT_29764 Reactome:REACT_30149 Reactome:REACT_31024 Reactome:REACT_31919 Reactome:REACT_32546 Reactome:REACT_32932 Reactome:REACT_33572 Reactome:REACT_33874 Reactome:REACT_50018 Reactome:REACT_53588 Reactome:REACT_6729 Reactome:REACT_6738 Reactome:REACT_6750 Reactome:REACT_6769 Reactome:REACT_6798 Reactome:REACT_6869 Reactome:REACT_6936 Reactome:REACT_6939 Reactome:REACT_77532 Reactome:REACT_79188 Reactome:REACT_79450 Reactome:REACT_80432 Reactome:REACT_80571 Reactome:REACT_80896 Reactome:REACT_80988 Reactome:REACT_81803 Reactome:REACT_83095 Reactome:REACT_84829 Reactome:REACT_85561 Reactome:REACT_86410 Reactome:REACT_86739 Reactome:REACT_87233 Reactome:REACT_87449 Reactome:REACT_87590 Reactome:REACT_88085 Reactome:REACT_88384 Reactome:REACT_88529 Reactome:REACT_89355 Reactome:REACT_89439 Reactome:REACT_89725 Reactome:REACT_90512 Reactome:REACT_90809 Reactome:REACT_90838 Reactome:REACT_91184 Reactome:REACT_91302 Reactome:REACT_92527 Reactome:REACT_92644 Reactome:REACT_92706 Reactome:REACT_94983 Reactome:REACT_95253 Reactome:REACT_95329 Reactome:REACT_96115 Reactome:REACT_96804 Reactome:REACT_96998 Reactome:REACT_97204 Reactome:REACT_97726 Reactome:REACT_99948 Wikipedia:DNA_replication biological_process GO:0006260 See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'. DNA replication The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. GOC:mah Reactome:REACT_100559 Activation of ATR in response to replication stress, Mus musculus Reactome:REACT_101280 Activation of claspin, Xenopus tropicalis Reactome:REACT_101497 Activation of claspin, Bos taurus Reactome:REACT_102679 Activation of ATR in response to replication stress, Gallus gallus Reactome:REACT_103614 Stalling of DNA replication fork and RPA binding, Taeniopygia guttata Reactome:REACT_104547 Recruitment and activation of Chk1, Gallus gallus Reactome:REACT_105292 Activation of ATR in response to replication stress, Xenopus tropicalis Reactome:REACT_105467 Loading of claspin onto DNA during replication origin firing, Danio rerio Reactome:REACT_105835 Stalling of DNA replication fork and RPA binding, Gallus gallus Reactome:REACT_106018 Recruitment of Rad17-RFC complex to DNA, Gallus gallus Reactome:REACT_106104 Binding of ATR-ATRIP to the RPA-ssDNA complex, Bos taurus Reactome:REACT_106382 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Drosophila melanogaster Reactome:REACT_106434 Activation of claspin, Canis familiaris Reactome:REACT_106732 Recruitment and activation of Chk1, Canis familiaris Reactome:REACT_107075 Activation of ATR in response to replication stress, Danio rerio Reactome:REACT_107423 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Caenorhabditis elegans Reactome:REACT_108461 Recruitment and activation of Chk1, Bos taurus Reactome:REACT_108634 Loading of claspin onto DNA during replication origin firing, Mus musculus Reactome:REACT_108739 Binding of ATR-ATRIP to the RPA-ssDNA complex, Xenopus tropicalis Reactome:REACT_108768 Activation of ATR in response to replication stress, Bos taurus Reactome:REACT_108929 Activation of ATR in response to replication stress, Drosophila melanogaster Reactome:REACT_109137 Stalling of DNA replication fork and RPA binding, Rattus norvegicus Reactome:REACT_112472 Activation of ATR in response to replication stress, Saccharomyces cerevisiae Reactome:REACT_113703 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Gallus gallus Reactome:REACT_29423 Activation of ATR in response to replication stress, Schizosaccharomyces pombe Reactome:REACT_29444 Binding of ATR-ATRIP to the RPA-ssDNA complex, Taeniopygia guttata Reactome:REACT_29691 Activation of ATR in response to replication stress, Rattus norvegicus Reactome:REACT_29764 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Taeniopygia guttata Reactome:REACT_30149 Activation of claspin, Rattus norvegicus Reactome:REACT_31024 Recruitment of Rad17-RFC complex to DNA, Xenopus tropicalis Reactome:REACT_31919 Loading of claspin onto DNA during replication origin firing, Rattus norvegicus Reactome:REACT_32546 Recruitment of Rad17-RFC complex to DNA, Mus musculus Reactome:REACT_32932 Recruitment and activation of Chk1, Taeniopygia guttata Reactome:REACT_33572 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Dictyostelium discoideum Reactome:REACT_33874 Recruitment and activation of Chk1, Xenopus tropicalis Reactome:REACT_50018 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Rattus norvegicus Reactome:REACT_53588 Loading of claspin onto DNA during replication origin firing, Canis familiaris Reactome:REACT_6729 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Homo sapiens Reactome:REACT_6738 Loading of claspin onto DNA during replication origin firing, Homo sapiens Reactome:REACT_6750 Activation of claspin, Homo sapiens Reactome:REACT_6769 Activation of ATR in response to replication stress, Homo sapiens Reactome:REACT_6798 Recruitment of Rad17-RFC complex to DNA, Homo sapiens Reactome:REACT_6869 Recruitment and activation of Chk1, Homo sapiens Reactome:REACT_6936 Stalling of DNA replication fork and RPA binding, Homo sapiens Reactome:REACT_6939 Binding of ATR-ATRIP to the RPA-ssDNA complex, Homo sapiens Reactome:REACT_77532 Stalling of DNA replication fork and RPA binding, Canis familiaris Reactome:REACT_79188 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Canis familiaris Reactome:REACT_79450 Activation of ATR in response to replication stress, Dictyostelium discoideum Reactome:REACT_80432 Loading of claspin onto DNA during replication origin firing, Taeniopygia guttata Reactome:REACT_80571 Activation of claspin, Mus musculus Reactome:REACT_80896 Recruitment and activation of Chk1, Sus scrofa Reactome:REACT_80988 Loading of claspin onto DNA during replication origin firing, Bos taurus Reactome:REACT_81803 Recruitment of Rad17-RFC complex to DNA, Canis familiaris Reactome:REACT_83095 Recruitment of Rad17-RFC complex to DNA, Danio rerio Reactome:REACT_84829 Binding of ATR-ATRIP to the RPA-ssDNA complex, Danio rerio Reactome:REACT_85561 Binding of ATR-ATRIP to the RPA-ssDNA complex, Rattus norvegicus Reactome:REACT_86410 Stalling of DNA replication fork and RPA binding, Mus musculus Reactome:REACT_86739 Recruitment and activation of Chk1, Rattus norvegicus Reactome:REACT_87233 Binding of ATR-ATRIP to the RPA-ssDNA complex, Canis familiaris Reactome:REACT_87449 Recruitment of Rad17-RFC complex to DNA, Rattus norvegicus Reactome:REACT_87590 Recruitment of Rad17-RFC complex to DNA, Bos taurus Reactome:REACT_88085 Binding of ATR-ATRIP to the RPA-ssDNA complex, Gallus gallus Reactome:REACT_88384 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Schizosaccharomyces pombe Reactome:REACT_88529 Activation of claspin, Gallus gallus Reactome:REACT_89355 Activation of claspin, Danio rerio Reactome:REACT_89439 Activation of ATR in response to replication stress, Sus scrofa Reactome:REACT_89725 Loading of claspin onto DNA during replication origin firing, Drosophila melanogaster Reactome:REACT_90512 Stalling of DNA replication fork and RPA binding, Bos taurus Reactome:REACT_90809 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Danio rerio Reactome:REACT_90838 Recruitment of Rad17-RFC complex to DNA, Taeniopygia guttata Reactome:REACT_91184 Recruitment and activation of Chk1, Danio rerio Reactome:REACT_91302 Activation of ATR in response to replication stress, Canis familiaris Reactome:REACT_92527 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Mus musculus Reactome:REACT_92644 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Xenopus tropicalis Reactome:REACT_92706 Stalling of DNA replication fork and RPA binding, Danio rerio Reactome:REACT_94983 Stalling of DNA replication fork and RPA binding, Xenopus tropicalis Reactome:REACT_95253 Activation of ATR in response to replication stress, Taeniopygia guttata Reactome:REACT_95329 Activation of claspin, Taeniopygia guttata Reactome:REACT_96115 Binding of ATR-ATRIP to the RPA-ssDNA complex, Mus musculus Reactome:REACT_96804 Recruitment and activation of Chk1, Mus musculus Reactome:REACT_96998 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Bos taurus Reactome:REACT_97204 Loading of claspin onto DNA during replication origin firing, Gallus gallus Reactome:REACT_97726 Activation of ATR in response to replication stress, Caenorhabditis elegans Reactome:REACT_99948 Loading of claspin onto DNA during replication origin firing, Xenopus tropicalis The process in which the number of copies of a gene is increased in certain cells as extra copies of DNA are made in response to certain signals of cell development or of stress from the environment. biological_process GO:0006277 DNA amplification The process in which the number of copies of a gene is increased in certain cells as extra copies of DNA are made in response to certain signals of cell development or of stress from the environment. ISBN:0721601464 A DNA replication process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strands. Reactome:REACT_6880 Reactome:REACT_9037 Reactome:REACT_9055 biological_process GO:0006278 RNA-dependent DNA replication A DNA replication process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strands. GOC:mah ISBN:0198506732 Reactome:REACT_6880 Reverse Transcription of HIV RNA, Homo sapiens Reactome:REACT_9037 Plus-strand DNA synthesis, Homo sapiens Reactome:REACT_9055 Minus-strand DNA synthesis, Homo sapiens The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. DNA breakdown DNA catabolism DNA degradation biological_process GO:0006308 DNA catabolic process The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. GOC:go_curators ISBN:0198506732 The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments. GO:0008178 DNA fragmentation chromatinolysis Reactome:REACT_102783 Reactome:REACT_105342 Reactome:REACT_110358 Reactome:REACT_113418 Reactome:REACT_1213 Reactome:REACT_28808 Reactome:REACT_33113 Reactome:REACT_92967 Reactome:REACT_94135 Reactome:REACT_98713 Reactome:REACT_99275 Reactome:REACT_99925 DNA catabolic process during apoptosis DNA catabolism during apoptosis DNA fragmentation involved in apoptotic nuclear change endonucleolytic DNA catabolic process involved in apoptosis biological_process GO:0006309 DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases. In human, these include DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G) (reviewed in PMID:15723341). Caution is needed when apoptotic DNA laddering assays show presence of fragmented DNA. A positive assay may simply reflect the end point of a whole apoptotic process. Unless clear experimental evidence is available to show that a gene product is directly involved in fragmenting DNA, please do not annotate to GO:0006309 'apoptotic DNA fragmentation' and consider annotating instead to a more upstream process such as, e.g., GO:0042981 'regulation of apoptotic process', GO:0006915 'apoptotic process', GO:0097190 'apoptotic signaling pathway'. Also, note that gene products involved in compartmentalization of apoptotic nucleases and in activation or repression of their enzymatic activity should be annotated to the regulation term GO:1902510 'regulation of apoptotic DNA fragmentation' or to one of its children (see PMID:15723341). apoptotic DNA fragmentation The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments. GOC:dph GOC:mah GOC:mtg_apoptosis GOC:tb ISBN:0721639976 PMID:15723341 PMID:23379520 chromatinolysis GOC:mtg_apoptosis Reactome:REACT_102783 Apoptosis induced DNA fragmentation, Bos taurus Reactome:REACT_105342 Apoptosis induced DNA fragmentation, Sus scrofa Reactome:REACT_110358 Apoptosis induced DNA fragmentation, Xenopus tropicalis Reactome:REACT_113418 Apoptosis induced DNA fragmentation, Plasmodium falciparum Reactome:REACT_1213 Apoptosis induced DNA fragmentation, Homo sapiens Reactome:REACT_28808 Apoptosis induced DNA fragmentation, Rattus norvegicus Reactome:REACT_33113 Apoptosis induced DNA fragmentation, Mus musculus Reactome:REACT_92967 Apoptosis induced DNA fragmentation, Drosophila melanogaster Reactome:REACT_94135 Apoptosis induced DNA fragmentation, Taeniopygia guttata Reactome:REACT_98713 Apoptosis induced DNA fragmentation, Canis familiaris Reactome:REACT_99275 Apoptosis induced DNA fragmentation, Gallus gallus Reactome:REACT_99925 Apoptosis induced DNA fragmentation, Danio rerio DNA fragmentation involved in apoptotic nuclear change GOC:cjm GOC:dph GOC:tb Any process in which DNA and associated proteins are formed into a compact, orderly structure. DNA condensation DNA organisation DNA organization biological_process GO:0006323 DNA packaging Any process in which DNA and associated proteins are formed into a compact, orderly structure. GOC:mah ISBN:0815316194 DNA organisation GOC:curators DNA organization GOC:curators The cellular synthesis of RNA on a template of DNA. GO:0006350 GO:0061018 GO:0061022 cellular transcription transcription Wikipedia:Transcription_(genetics) DNA-dependent transcription cellular transcription, DNA-dependent transcription, DNA-dependent biological_process transcription regulator activity GO:0006351 transcription, DNA-templated The cellular synthesis of RNA on a template of DNA. GOC:jl GOC:txnOH transcription, DNA-dependent GOC:txnOH Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0032583 GO:0045449 GO:0061019 transcriptional control regulation of cellular transcription, DNA-dependent regulation of transcription, DNA-dependent biological_process regulation of gene-specific transcription GO:0006355 regulation of transcription, DNA-templated Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GOC:go_curators GOC:txnOH regulation of transcription, DNA-dependent GOC:txnOH The process of targeting specific proteins to particular membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif. Wikipedia:Protein_targeting protein sorting along secretory pathway biological_process nascent polypeptide association GO:0006605 Note that protein targeting encompasses the transport of the protein to the specified location, and may also include additional steps such as protein processing. protein targeting The process of targeting specific proteins to particular membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif. GOC:ma The directed movement of a protein from the cytoplasm to the nucleus. establishment of protein localization to nucleus protein import into cell nucleus protein nucleus import protein transport from cytoplasm to nucleus biological_process GO:0006606 protein import into nucleus The directed movement of a protein from the cytoplasm to the nucleus. GOC:jl establishment of protein localization to nucleus GOC:mah The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. aromatic compound metabolism aromatic hydrocarbon metabolic process aromatic hydrocarbon metabolism biological_process GO:0006725 cellular aromatic compound metabolic process The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. GOC:ai ISBN:0198506732 The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium. nitrogen compound metabolism biological_process GO:0006807 Note that amino acid and derivative metabolism should not be annotated here. Instead use the 'amino acid and derivative metabolism' node. nitrogen compound metabolic process The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium. CHEBI:51143 GOC:go_curators GOC:jl ISBN:0198506732 The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. GO:0015457 GO:0015460 small molecule transport solute:solute exchange biological_process auxiliary transport protein activity transport accessory protein activity GO:0006810 transport The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. GOC:dph GOC:jl GOC:mah auxiliary transport protein activity GOC:mah transport accessory protein activity GOC:mah The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GO:0032779 biological_process copper-induced intracellular protein transport GO:0006886 intracellular protein transport The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GOC:mah copper-induced intracellular protein transport GOC:al The directed movement of molecules between the nucleus and the cytoplasm. GO:0000063 nucleocytoplasmic shuttling biological_process GO:0006913 Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed. nucleocytoplasmic transport The directed movement of molecules between the nucleus and the cytoplasm. GOC:go_curators A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GO:0006917 GO:0008632 cell suicide cellular suicide Reactome:REACT_100045 Reactome:REACT_100962 Reactome:REACT_101249 Reactome:REACT_104187 Reactome:REACT_105149 Reactome:REACT_106405 Reactome:REACT_106672 Reactome:REACT_107264 Reactome:REACT_108651 Reactome:REACT_109165 Reactome:REACT_110081 Reactome:REACT_111964 Reactome:REACT_13526 Reactome:REACT_13638 Reactome:REACT_13643 Reactome:REACT_28087 Reactome:REACT_28795 Reactome:REACT_28816 Reactome:REACT_30266 Reactome:REACT_30361 Reactome:REACT_30371 Reactome:REACT_30548 Reactome:REACT_30763 Reactome:REACT_31349 Reactome:REACT_34139 Reactome:REACT_578 Reactome:REACT_77132 Reactome:REACT_77313 Reactome:REACT_77415 Reactome:REACT_78287 Reactome:REACT_78802 Reactome:REACT_79809 Reactome:REACT_82724 Reactome:REACT_83328 Reactome:REACT_85877 Reactome:REACT_86749 Reactome:REACT_86873 Reactome:REACT_87570 Reactome:REACT_88740 Reactome:REACT_88784 Reactome:REACT_89196 Reactome:REACT_90267 Reactome:REACT_91011 Reactome:REACT_91243 Reactome:REACT_93937 Reactome:REACT_94099 Reactome:REACT_95069 Reactome:REACT_95675 Reactome:REACT_97627 Reactome:REACT_99784 Reactome:REACT_99799 Wikipedia:Apoptosis apoptotic cell death apoptotic programmed cell death programmed cell death by apoptosis activation of apoptosis apoptosis apoptosis signaling apoptotic program type I programmed cell death biological_process apoptosis activator activity commitment to apoptosis induction of apoptosis induction of apoptosis by p53 signaling (initiator) caspase activity GO:0006915 apoptotic process A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GOC:dhl GOC:ecd GOC:go_curators GOC:mtg_apoptosis GOC:tb ISBN:0198506732 PMID:18846107 PMID:21494263 Reactome:REACT_100045 Apoptosis, Drosophila melanogaster Reactome:REACT_100962 Apoptosis, Mus musculus Reactome:REACT_101249 NRIF signals cell death from the nucleus, Danio rerio Reactome:REACT_104187 NRAGE signals death through JNK, Taeniopygia guttata Reactome:REACT_105149 NADE modulates death signalling, Rattus norvegicus Reactome:REACT_106405 NRAGE signals death through JNK, Xenopus tropicalis Reactome:REACT_106672 NADE modulates death signalling, Sus scrofa Reactome:REACT_107264 NRIF signals cell death from the nucleus, Xenopus tropicalis Reactome:REACT_108651 NRAGE signals death through JNK, Mus musculus Reactome:REACT_109165 NRAGE signals death through JNK, Arabidopsis thaliana Reactome:REACT_110081 NRAGE signals death through JNK, Schizosaccharomyces pombe Reactome:REACT_111964 NRAGE signals death through JNK, Dictyostelium discoideum Reactome:REACT_13526 NADE modulates death signalling, Homo sapiens Reactome:REACT_13638 NRAGE signals death through JNK, Homo sapiens Reactome:REACT_13643 NRIF signals cell death from the nucleus, Homo sapiens Reactome:REACT_28087 Apoptosis, Saccharomyces cerevisiae Reactome:REACT_28795 Apoptosis, Oryza sativa Reactome:REACT_28816 Apoptosis, Danio rerio Reactome:REACT_30266 Apoptosis, Arabidopsis thaliana Reactome:REACT_30361 Apoptosis, Canis familiaris Reactome:REACT_30371 NRAGE signals death through JNK, Saccharomyces cerevisiae Reactome:REACT_30548 NRAGE signals death through JNK, Caenorhabditis elegans Reactome:REACT_30763 NRAGE signals death through JNK, Oryza sativa Reactome:REACT_31349 NRAGE signals death through JNK, Canis familiaris Reactome:REACT_34139 NRAGE signals death through JNK, Gallus gallus Reactome:REACT_578 Apoptosis, Homo sapiens Reactome:REACT_77132 NRAGE signals death through JNK, Drosophila melanogaster Reactome:REACT_77313 NADE modulates death signalling, Bos taurus Reactome:REACT_77415 NRIF signals cell death from the nucleus, Canis familiaris Reactome:REACT_78287 Apoptosis, Gallus gallus Reactome:REACT_78802 NADE modulates death signalling, Canis familiaris Reactome:REACT_79809 Apoptosis, Schizosaccharomyces pombe Reactome:REACT_82724 Apoptosis, Taeniopygia guttata Reactome:REACT_83328 Apoptosis, Sus scrofa Reactome:REACT_85877 NRAGE signals death through JNK, Rattus norvegicus Reactome:REACT_86749 Apoptosis, Rattus norvegicus Reactome:REACT_86873 NRIF signals cell death from the nucleus, Gallus gallus Reactome:REACT_87570 NRIF signals cell death from the nucleus, Rattus norvegicus Reactome:REACT_88740 NRIF signals cell death from the nucleus, Sus scrofa Reactome:REACT_88784 NRIF signals cell death from the nucleus, Mus musculus Reactome:REACT_89196 Apoptosis, Dictyostelium discoideum Reactome:REACT_90267 NRIF signals cell death from the nucleus, Taeniopygia guttata Reactome:REACT_91011 Apoptosis, Caenorhabditis elegans Reactome:REACT_91243 NADE modulates death signalling, Mus musculus Reactome:REACT_93937 Apoptosis, Bos taurus Reactome:REACT_94099 NRAGE signals death through JNK, Danio rerio Reactome:REACT_95069 Apoptosis, Xenopus tropicalis Reactome:REACT_95675 Apoptosis, Plasmodium falciparum Reactome:REACT_97627 NRIF signals cell death from the nucleus, Bos taurus Reactome:REACT_99784 NRAGE signals death through JNK, Bos taurus Reactome:REACT_99799 NRAGE signals death through JNK, Sus scrofa apoptotic cell death GOC:sl apoptotic program GOC:add The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis. cellular component disassembly involved in apoptotic process disassembly of cell structures Reactome:REACT_100800 Reactome:REACT_108463 Reactome:REACT_29660 Reactome:REACT_77151 Reactome:REACT_78666 Reactome:REACT_79472 Reactome:REACT_79859 Reactome:REACT_80493 Reactome:REACT_81021 Reactome:REACT_81052 Reactome:REACT_84120 Reactome:REACT_89424 Reactome:REACT_90988 Reactome:REACT_92689 Reactome:REACT_93576 Reactome:REACT_94230 Reactome:REACT_97703 Reactome:REACT_995 cellular component disassembly involved in apoptosis biological_process GO:0006921 cellular component disassembly involved in execution phase of apoptosis The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis. GOC:dph GOC:mah GOC:mtg_apoptosis GOC:tb Reactome:REACT_100800 Apoptotic execution phase, Danio rerio Reactome:REACT_108463 Apoptotic execution phase, Taeniopygia guttata Reactome:REACT_29660 Apoptotic execution phase, Oryza sativa Reactome:REACT_77151 Apoptotic execution phase, Sus scrofa Reactome:REACT_78666 Apoptotic execution phase, Saccharomyces cerevisiae Reactome:REACT_79472 Apoptotic execution phase, Schizosaccharomyces pombe Reactome:REACT_79859 Apoptotic execution phase, Rattus norvegicus Reactome:REACT_80493 Apoptotic execution phase, Dictyostelium discoideum Reactome:REACT_81021 Apoptotic execution phase, Drosophila melanogaster Reactome:REACT_81052 Apoptotic execution phase, Canis familiaris Reactome:REACT_84120 Apoptotic execution phase, Xenopus tropicalis Reactome:REACT_89424 Apoptotic execution phase, Arabidopsis thaliana Reactome:REACT_90988 Apoptotic execution phase, Plasmodium falciparum Reactome:REACT_92689 Apoptotic execution phase, Caenorhabditis elegans Reactome:REACT_93576 Apoptotic execution phase, Gallus gallus Reactome:REACT_94230 Apoptotic execution phase, Bos taurus Reactome:REACT_97703 Apoptotic execution phase, Mus musculus Reactome:REACT_995 Apoptotic execution phase, Homo sapiens The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore. cellular component motion cellular component movement biological_process cell movement GO:0006928 Note that in GO cellular components include whole cells (cell is_a cellular component). movement of cell or subcellular component The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore. GOC:dgh GOC:dph GOC:jl GOC:mlg cellular component motion GOC:dph GOC:jl The orderly movement of a cell from one site to another along a substrate such as the extracellular matrix; the migrating cell forms a protrusion that attaches to the substrate. substrate-bound cell migration biological_process GO:0006929 substrate-dependent cell migration The orderly movement of a cell from one site to another along a substrate such as the extracellular matrix; the migrating cell forms a protrusion that attaches to the substrate. ISBN:0815316194 PMID:11944043 PMID:14657486 substrate-bound cell migration GOC:curators The formation of a cell surface protrusion, such as a lamellipodium or filopodium, at the leading edge of a migrating cell. substrate-bound cell migration, cell extension biological_process GO:0006930 substrate-dependent cell migration, cell extension The formation of a cell surface protrusion, such as a lamellipodium or filopodium, at the leading edge of a migrating cell. ISBN:0815316194 PMID:11944043 PMID:14657486 substrate-bound cell migration, cell extension GOC:curators Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). biological_process response to abiotic stress response to biotic stress GO:0006950 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stress Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:mah Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. biological_process GO:0006955 This term was improved by GO_REF:0000022. It was redefined and moved. immune response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. GOC:add GOC:mtg_15nov05 GO_REF:0000022 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. GO:0034984 response to DNA damage stimulus DNA damage response cellular DNA damage response response to genotoxic stress biological_process GO:0006974 cellular response to DNA damage stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. GOC:go_curators A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. organelle organisation biological_process organelle organization and biogenesis GO:0006996 organelle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:mah organelle organisation GOC:curators organelle organization and biogenesis GOC:dph GOC:jl GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus. GO:0048287 nuclear organisation nuclear organization biological_process nuclear morphology nuclear organization and biogenesis nucleus organization and biogenesis GO:0006997 nucleus organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus. GOC:dph GOC:ems GOC:jl GOC:mah nuclear organisation GOC:curators nuclear organization GOC:curators nuclear organization and biogenesis GOC:mah nucleus organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope. nuclear envelope organisation biological_process nuclear envelope organization and biogenesis GO:0006998 nuclear envelope organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope. GOC:dph GOC:ems GOC:jl GOC:mah nuclear envelope organisation GOC:mah nuclear envelope organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. plasma membrane organisation biological_process plasma membrane organization and biogenesis GO:0007009 plasma membrane organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. GOC:dph GOC:jl GOC:mah plasma membrane organisation GOC:curators plasma membrane organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. cytoskeleton organisation biological_process cytoskeletal organization and biogenesis cytoskeletal regulator activity cytoskeleton organization and biogenesis GO:0007010 cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:dph GOC:jl GOC:mah cytoskeleton organisation GOC:curators cytoskeletal organization and biogenesis GOC:mah cytoskeleton organization and biogenesis GOC:mah Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. biological_process GO:0007017 microtubule-based process Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endoplasmic reticulum. ER organisation endoplasmic reticulum organisation biological_process ER organization and biogenesis endoplasmic reticulum morphology endoplasmic reticulum organization and biogenesis GO:0007029 endoplasmic reticulum organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endoplasmic reticulum. GOC:dph GOC:jl GOC:mah ER organisation GOC:curators endoplasmic reticulum organisation GOC:curators ER organization and biogenesis GOC:mah endoplasmic reticulum organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules. peroxisome organisation biological_process peroxisome organization and biogenesis peroxisome-assembly ATPase activity GO:0007031 peroxisome organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules. GOC:mah peroxisome organisation GOC:curators peroxisome organization and biogenesis GOC:mah The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. Wikipedia:Cell_cycle cell-division cycle biological_process GO:0007049 cell cycle The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. GOC:go_curators GOC:mtg_cell_cycle The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. Wikipedia:Chromosome_segregation chromosome division biological_process chromosome transmission GO:0007059 chromosome segregation The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. GOC:jl GOC:mah GOC:mtg_cell_cycle GOC:vw A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. Wikipedia:Mitosis mitosis biological_process GO:0007067 mitotic nuclear division A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. GOC:dph GOC:ma GOC:mah ISBN:0198547684 The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells. biological_process GO:0007076 mitotic chromosome condensation The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells. GOC:mah ISBN:0815316194 The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis. biological_process GO:0007080 mitotic metaphase plate congression The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis. GOC:mah ISBN:0815316194 The cell cycle process in which chromosome structure is altered from the condensed form taken on during mitosis to the relaxed disperse form held in resting cells. biological_process GO:0007083 mitotic chromosome decondensation The cell cycle process in which chromosome structure is altered from the condensed form taken on during mitosis to the relaxed disperse form held in resting cells. GOC:ai The cell cycle process in which centrosome duplication and separation takes place. The centrosome cycle can operate with a considerable degree of independence from other processes of the cell cycle. biological_process GO:0007098 centrosome cycle The cell cycle process in which centrosome duplication and separation takes place. The centrosome cycle can operate with a considerable degree of independence from other processes of the cell cycle. ISBN:0815316194 The cell cycle process in which a daughter centriole is formed perpendicular to an existing centriole. An immature centriole contains a ninefold radially symmetric array of single microtubules; mature centrioles consist of a radial array of nine microtubule triplets, doublets, or singlets depending upon the species and cell type. centriole duplication biological_process GO:0007099 centriole replication The cell cycle process in which a daughter centriole is formed perpendicular to an existing centriole. An immature centriole contains a ninefold radially symmetric array of single microtubules; mature centrioles consist of a radial array of nine microtubule triplets, doublets, or singlets depending upon the species and cell type. GOC:kmv ISBN:0815316194 Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. Wikipedia:Cell_signaling biological_process GO:0007154 cell communication Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:mah The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. Wikipedia:Cell_adhesion biological_process cell adhesion molecule activity GO:0007155 cell adhesion The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. GOC:hb GOC:pf The binding of a cell to the extracellular matrix via adhesion molecules. biological_process GO:0007160 cell-matrix adhesion The binding of a cell to the extracellular matrix via adhesion molecules. GOC:hb Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns. GO:0030012 GO:0030467 biological_process cell polarity establishment and/or maintenance of cell polarity establishment and/or maintenance of cell polarization GO:0007163 establishment or maintenance of cell polarity Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns. GOC:mah cell polarity GOC:mah GOC:vw The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GO:0023033 Reactome:REACT_100624 Reactome:REACT_102354 Reactome:REACT_112130 Reactome:REACT_112549 Reactome:REACT_113151 Reactome:REACT_113601 Reactome:REACT_113964 Reactome:REACT_114657 Reactome:REACT_114690 Reactome:REACT_114820 Reactome:REACT_114910 Reactome:REACT_115037 Reactome:REACT_115147 Reactome:REACT_12478 Reactome:REACT_31232 Reactome:REACT_78535 Reactome:REACT_89740 Reactome:REACT_93680 Reactome:REACT_98872 Wikipedia:Signal_transduction signaling cascade signalling cascade biological_process signaling pathway signalling pathway GO:0007165 Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. signal transduction The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GOC:go_curators GOC:mtg_signaling_feb11 Reactome:REACT_100624 EGFR interacts with phospholipase C-gamma, Gallus gallus Reactome:REACT_102354 EGFR interacts with phospholipase C-gamma, Canis familiaris Reactome:REACT_112130 EGFR interacts with phospholipase C-gamma, Oryza sativa Reactome:REACT_112549 EGFR interacts with phospholipase C-gamma, Arabidopsis thaliana Reactome:REACT_113151 EGFR interacts with phospholipase C-gamma, Mycobacterium tuberculosis Reactome:REACT_113601 EGFR interacts with phospholipase C-gamma, Drosophila melanogaster Reactome:REACT_113964 EGFR interacts with phospholipase C-gamma, Bos taurus Reactome:REACT_114657 EGFR interacts with phospholipase C-gamma, Dictyostelium discoideum Reactome:REACT_114690 EGFR interacts with phospholipase C-gamma, Saccharomyces cerevisiae Reactome:REACT_114820 EGFR interacts with phospholipase C-gamma, Sus scrofa Reactome:REACT_114910 EGFR interacts with phospholipase C-gamma, Caenorhabditis elegans Reactome:REACT_115037 EGFR interacts with phospholipase C-gamma, Plasmodium falciparum Reactome:REACT_115147 EGFR interacts with phospholipase C-gamma, Schizosaccharomyces pombe Reactome:REACT_12478 EGFR interacts with phospholipase C-gamma, Homo sapiens Reactome:REACT_31232 EGFR interacts with phospholipase C-gamma, Rattus norvegicus Reactome:REACT_78535 EGFR interacts with phospholipase C-gamma, Xenopus tropicalis Reactome:REACT_89740 EGFR interacts with phospholipase C-gamma, Taeniopygia guttata Reactome:REACT_93680 EGFR interacts with phospholipase C-gamma, Danio rerio Reactome:REACT_98872 EGFR interacts with phospholipase C-gamma, Mus musculus signalling pathway GOC:mah The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription. NF-kappaB cascade Reactome:REACT_13696.1 Reactome:REACT_25351 I-kappaB kinase/NF-kappaB signal transduction canonical NF-kappaB signaling cascade biological_process I-kappaB kinase/NF-kappaB cascade activation of the inhibitor of kappa kinase p50-dependent NF-kappaB signaling GO:0007249 I-kappaB kinase/NF-kappaB signaling The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription. GOC:bf GOC:jl PMID:12773372 Reactome:REACT_13696.1 Reactome:REACT_13696.1 NF-kB is activated and signals survival, Homo sapiens Reactome:REACT_25351 TRAF6 mediated induction of TAK1 complex, Homo sapiens I-kappaB kinase/NF-kappaB signal transduction GOC:signaling canonical NF-kappaB signaling cascade GOC:bf I-kappaB kinase/NF-kappaB cascade GOC:signaling p50-dependent NF-kappaB signaling PMID:18292232 The selective interaction of the transcription factor NF-kappaB with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus. cytoplasmic NF-kappaB retention cytoplasmic NF-kappaB sequestration cytoplasmic NF-kappaB storage cytoplasmic retention of NF-kappaB cytoplasmic sequestration of NF-kappaB cytoplasmic storage of NF-kappaB maintenance of NF-kappaB location in cytoplasm biological_process GO:0007253 cytoplasmic sequestering of NF-kappaB The selective interaction of the transcription factor NF-kappaB with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus. GOC:jl maintenance of NF-kappaB location in cytoplasm GOC:dph GOC:tb Any process in which a protein is transported to, or maintained in, a specific location. establishment and maintenance of protein localization protein localisation biological_process GO:0008104 protein localization Any process in which a protein is transported to, or maintained in, a specific location. GOC:ai protein localisation GOC:mah Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. GO:0000004 GO:0007582 Wikipedia:Biological_process biological process physiological process biological_process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. GOC:go_curators GOC:isa_complete The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth biological_process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. GOC:go_curators ISBN:0198547684 Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as "apoptotic bodies"); and/or (3) its corpse (or its fragments) have been engulfed by an adjacent cell in vivo. biological_process accidental cell death necrosis GO:0008219 This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term. cell death Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as "apoptotic bodies"); and/or (3) its corpse (or its fragments) have been engulfed by an adjacent cell in vivo. GOC:mah GOC:mtg_apoptosis The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence. DNA bending activity DNA bending involving DNA binding molecular_function GO:0008301 DNA binding, bending The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence. GOC:krc GOC:vw PMID:10710711 PMID:19037758 The release of NF-kappaB from specific molecules in the cytoplasm to which it was bound, thereby allowing its translocation into the nucleus. release of NF-kappaB sequestered in cytoplasm release of NF-kappaB stored in cytoplasm biological_process activation of NF-kappa B negative regulation of cytoplasmic NF-kappaB retention negative regulation of cytoplasmic NF-kappaB sequestering negative regulation of cytoplasmic NF-kappaB sequestration negative regulation of cytoplasmic NF-kappaB storage GO:0008588 release of cytoplasmic sequestered NF-kappaB The release of NF-kappaB from specific molecules in the cytoplasm to which it was bound, thereby allowing its translocation into the nucleus. GOC:jl The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. Wikipedia:Catabolism breakdown catabolism degradation biological_process GO:0009056 catabolic process The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. ISBN:0198547684 The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0043285 biopolymer catabolic process macromolecule breakdown macromolecule catabolism macromolecule degradation biological_process GO:0009057 macromolecule catabolic process The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. CHEBI:33694 GOC:mah biopolymer catabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. Wikipedia:Anabolism anabolism biosynthesis formation synthesis biological_process GO:0009058 biosynthetic process The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis macromolecule formation macromolecule synthesis biological_process GO:0009059 macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. CHEBI:33694 GOC:mah biopolymer biosynthetic process GOC:mtg_chebi_dec09 The controlled release of proteins from a cell. GO:0045166 GO:0045731 glycoprotein secretion protein secretion during cell fate commitment protein secretion resulting in cell fate commitment biological_process GO:0009306 protein secretion The controlled release of proteins from a cell. GOC:ai Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism. response to biotic stress biological_process GO:0009607 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to biotic stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism. GOC:hb The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. embryogenesis and morphogenesis Wikipedia:Morphogenesis anatomical structure organization morphogenesis biological_process GO:0009653 anatomical structure morphogenesis The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. GOC:go_curators ISBN:0521436125 The process in which a cell irreversibly increases in size in one [spatial] dimension or along one axis, resulting in the morphogenesis of the cell. cell growth along one axis cell growth in one dimension cell morphogenesis by unidimensional growth polar cell growth polarized cell growth cell elongation biological_process GO:0009826 Unidimensional cell growth refers to a change in both cell size and cell shape. For cell shape changes where cell size is not affected, consider instead the term 'regulation of cell shape ; GO:0008360' and its children. unidimensional cell growth The process in which a cell irreversibly increases in size in one [spatial] dimension or along one axis, resulting in the morphogenesis of the cell. ISBN:0943088399 cell morphogenesis by unidimensional growth GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. regulation of anabolism regulation of biosynthesis regulation of formation regulation of synthesis biological_process GO:0009889 regulation of biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. down regulation of biosynthetic process down-regulation of biosynthetic process downregulation of biosynthetic process negative regulation of anabolism negative regulation of biosynthesis negative regulation of formation negative regulation of synthesis inhibition of biosynthetic process biological_process GO:0009890 negative regulation of biosynthetic process Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. positive regulation of anabolism positive regulation of biosynthesis positive regulation of formation positive regulation of synthesis up regulation of biosynthetic process up-regulation of biosynthetic process upregulation of biosynthetic process activation of biosynthetic process stimulation of biosynthetic process biological_process GO:0009891 positive regulation of biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process negative regulation of metabolism inhibition of metabolic process biological_process GO:0009892 negative regulation of metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. positive regulation of metabolism up regulation of metabolic process up-regulation of metabolic process upregulation of metabolic process activation of metabolic process stimulation of metabolic process biological_process GO:0009893 positive regulation of metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that modulates the frequency, rate or extent of signal transduction. GO:0035466 biological_process regulation of signaling pathway regulation of signalling pathway GO:0009966 regulation of signal transduction Any process that modulates the frequency, rate or extent of signal transduction. GOC:sm regulation of signalling pathway GOC:mah Any process that activates or increases the frequency, rate or extent of signal transduction. GO:0035468 Reactome:REACT_6227 up regulation of signal transduction up-regulation of signal transduction upregulation of signal transduction activation of signal transduction stimulation of signal transduction biological_process positive regulation of signaling pathway positive regulation of signalling pathway GO:0009967 positive regulation of signal transduction Any process that activates or increases the frequency, rate or extent of signal transduction. GOC:sm Reactome:REACT_6227 Activated DTOR also phosphorylates D4EBP, Drosophila melanogaster positive regulation of signalling pathway GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GO:0035467 Reactome:REACT_6334 down regulation of signal transduction down-regulation of signal transduction downregulation of signal transduction inhibition of signal transduction biological_process negative regulation of signaling pathway negative regulation of signalling pathway GO:0009968 negative regulation of signal transduction Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GOC:sm Reactome:REACT_6334 DTSC1 AND DTSC2 form a complex, Drosophila melanogaster negative regulation of signalling pathway GOC:mah Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0008151 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process GO:0009987 cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. endomembrane organization endomembrane system organisation biological_process GO:0010256 endomembrane system organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. GOC:mah GOC:sm endomembrane organization GOC:curators endomembrane system organisation GOC:mah The cell cycle transition where a cell leaves M phase and enters a new G1 phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place. mitotic exit biological_process GO:0010458 exit from mitosis The cell cycle transition where a cell leaves M phase and enters a new G1 phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place. GOC:dph GOC:tb The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. Reactome:REACT_100537 Reactome:REACT_101147 Reactome:REACT_101952 Reactome:REACT_105649 Reactome:REACT_108313 Reactome:REACT_29068 Reactome:REACT_34240 Reactome:REACT_71 Reactome:REACT_78136 Reactome:REACT_78959 Reactome:REACT_79662 Reactome:REACT_85241 Reactome:REACT_85359 Reactome:REACT_86357 Reactome:REACT_89816 Reactome:REACT_91657 Reactome:REACT_91965 Reactome:REACT_93586 Reactome:REACT_93968 Reactome:REACT_94814 Reactome:REACT_98256 Wikipedia:Gene_expression biological_process GO:0010467 gene expression The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb Reactome:REACT_100537 Gene Expression, Xenopus tropicalis Reactome:REACT_101147 Gene Expression, Danio rerio Reactome:REACT_101952 Gene Expression, Sus scrofa Reactome:REACT_105649 Gene Expression, Drosophila melanogaster Reactome:REACT_108313 Gene Expression, Caenorhabditis elegans Reactome:REACT_29068 Gene Expression, Escherichia coli Reactome:REACT_34240 Gene Expression, Staphylococcus aureus N315 Reactome:REACT_71 Gene Expression, Homo sapiens Reactome:REACT_78136 Gene Expression, Mus musculus Reactome:REACT_78959 Gene Expression, Taeniopygia guttata Reactome:REACT_79662 Gene Expression, Plasmodium falciparum Reactome:REACT_85241 Gene Expression, Oryza sativa Reactome:REACT_85359 Gene Expression, Gallus gallus Reactome:REACT_86357 Gene Expression, Canis familiaris Reactome:REACT_89816 Gene Expression, Mycobacterium tuberculosis Reactome:REACT_91657 Gene Expression, Arabidopsis thaliana Reactome:REACT_91965 Gene Expression, Rattus norvegicus Reactome:REACT_93586 Gene Expression, Dictyostelium discoideum Reactome:REACT_93968 Gene Expression, Bos taurus Reactome:REACT_94814 Gene Expression, Schizosaccharomyces pombe Reactome:REACT_98256 Gene Expression, Saccharomyces cerevisiae Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. Wikipedia:Regulation_of_gene_expression regulation of protein expression biological_process regulation of gene product expression GO:0010468 This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availabiliy of mRNA for translation and thereby regulates the rate of production of the encoded protein via translation. regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb regulation of protein expression GOC:curators regulation of gene product expression GOC:curators Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010556 regulation of macromolecule biosynthetic process Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010557 positive regulation of macromolecule biosynthetic process Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010558 negative regulation of macromolecule biosynthetic process Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010604 positive regulation of macromolecule metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010605 negative regulation of macromolecule metabolic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. biological_process GO:0010628 positive regulation of gene expression Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. biological_process GO:0010629 This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availabiliy of mRNA for translation and thereby reduces the rate of production of the encoded protein via translation. negative regulation of gene expression Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010646 regulation of cell communication Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010647 positive regulation of cell communication Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010648 negative regulation of cell communication Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. GO:0016244 Wikipedia:Programmed_cell_death PCD caspase-independent cell death non-apoptotic programmed cell death nonapoptotic programmed cell death biological_process caspase-independent apoptosis regulated cell death GO:0012501 Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children, which are descendants of GO:0034050 'host programmed cell death induced by symbiont'. programmed cell death A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. GOC:lr GOC:mtg_apoptosis A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. Wikipedia:Endomembrane_system cellular_component GO:0012505 endomembrane system A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. GOC:lh A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA. NIF_Subcellular:nlx_subcell_090901 Wikipedia:Cajal_body coiled body cellular_component Gemini of coiled bodies Gems GO:0015030 Cajal body A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA. NIF_Subcellular:nlx_subcell_090901 PMID:10944589 PMID:11031238 PMID:7559785 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015831 enzyme transport biological_process GO:0015031 protein transport The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. cellular_component GO:0015629 actin cytoskeleton The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. GOC:jl ISBN:0395825172 ISBN:0815316194 The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. cellular_component GO:0015630 microtubule cytoskeleton The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. GOC:jl ISBN:0395825172 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015833 peptide transport The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. Wikipedia:Biological_membrane cellular_component GO:0016020 membrane A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. GOC:dos GOC:mah ISBN:0815316194 A membrane-bounded vesicle found in the cytoplasm of the cell. cytoplasmic membrane bounded vesicle cytoplasmic membrane-enclosed vesicle cellular_component GO:0016023 cytoplasmic membrane-bounded vesicle A membrane-bounded vesicle found in the cytoplasm of the cell. GOC:ai GOC:mah A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0044235 GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism biological_process cell organization and biogenesis GO:0016043 cellular component organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:ai GOC:jl GOC:mah cellular component organisation at cellular level GOC:mah cellular component organisation in other organism GOC:mah cell organization and biogenesis GOC:mah The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. GO:0048591 cellular growth growth of cell biological_process cell expansion metabolic process resulting in cell growth metabolism resulting in cell growth non-developmental cell growth non-developmental growth of a unicellular organism GO:0016049 cell growth The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. GOC:ai non-developmental cell growth GOC:mah non-developmental growth of a unicellular organism GOC:mah The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Reactome:REACT_107259 Reactome:REACT_107652 Reactome:REACT_110289 Reactome:REACT_21257 Reactome:REACT_30579 Reactome:REACT_31367 Reactome:REACT_33720 Reactome:REACT_80071 Reactome:REACT_83630 Reactome:REACT_84169 Reactome:REACT_85788 Reactome:REACT_88316 Reactome:REACT_89992 Reactome:REACT_91556 Reactome:REACT_92152 Reactome:REACT_94876 Reactome:REACT_99403 Reactome:REACT_99885 RNA metabolism biological_process GO:0016070 RNA metabolic process The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. ISBN:0198506732 Reactome:REACT_107259 Metabolism of RNA, Sus scrofa Reactome:REACT_107652 Metabolism of RNA, Schizosaccharomyces pombe Reactome:REACT_110289 Metabolism of RNA, Danio rerio Reactome:REACT_21257 Metabolism of RNA, Homo sapiens Reactome:REACT_30579 Metabolism of RNA, Xenopus tropicalis Reactome:REACT_31367 Metabolism of RNA, Dictyostelium discoideum Reactome:REACT_33720 Metabolism of RNA, Plasmodium falciparum Reactome:REACT_80071 Metabolism of RNA, Caenorhabditis elegans Reactome:REACT_83630 Metabolism of RNA, Taeniopygia guttata Reactome:REACT_84169 Metabolism of RNA, Canis familiaris Reactome:REACT_85788 Metabolism of RNA, Oryza sativa Reactome:REACT_88316 Metabolism of RNA, Mus musculus Reactome:REACT_89992 Metabolism of RNA, Saccharomyces cerevisiae Reactome:REACT_91556 Metabolism of RNA, Bos taurus Reactome:REACT_92152 Metabolism of RNA, Drosophila melanogaster Reactome:REACT_94876 Metabolism of RNA, Arabidopsis thaliana Reactome:REACT_99403 Metabolism of RNA, Rattus norvegicus Reactome:REACT_99885 Metabolism of RNA, Gallus gallus A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism. Wikipedia:Death biological_process GO:0016265 This term should not be used for direct manual annotation. Instead, consider selecting a child term of GO:0008219 'cell death' or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. death A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism. GOC:mah GOC:mtg_apoptosis ISBN:0877797099 The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. Wikipedia:Cell_migration biological_process GO:0016477 cell migration The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. GOC:cjm GOC:dph GOC:ems GOC:pf http://en.wikipedia.org/wiki/Cell_migration The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, or within the cytoplasm of a cell. cytoplasmic streaming biological_process GO:0016482 cytoplasmic transport The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, or within the cytoplasm of a cell. GOC:ai Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. NIF_Subcellular:sao505137457 cellular_component GO:0016604 nuclear body Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. GOC:ma PMID:10330182 A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection. ND10 PML NB PML nuclear body cellular_component nuclear dot GO:0016605 PML body A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection. GOC:ma PMID:10944585 A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. nuclear speckle nuclear speckles splicing speckle speckle domain cellular_component speckle focus GO:0016607 nuclear speck A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. http://www.cellnucleus.com/ Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. EC:2 Reactome:REACT_25050 molecular_function GO:0016740 transferase activity Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. ISBN:0198506732 Reactome:REACT_25050 Molybdenum ion transfer onto molybdopterin, Homo sapiens Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). EC:2.7 molecular_function GO:0016772 Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. transferase activity, transferring phosphorus-containing groups Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 Catalysis of the transfer of a nucleotidyl group to a reactant. EC:2.7.7 molecular_function GO:0016779 nucleotidyltransferase activity Catalysis of the transfer of a nucleotidyl group to a reactant. ISBN:0198506732 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. EC:3 Reactome:REACT_110436 Reactome:REACT_111159 Reactome:REACT_15331 Reactome:REACT_83734 Reactome:REACT_84047 Reactome:REACT_87959 Reactome:REACT_88159 Reactome:REACT_90118 Reactome:REACT_91045 Reactome:REACT_98572 molecular_function GO:0016787 hydrolase activity Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. ISBN:0198506732 Reactome:REACT_110436 Hydrolysis of phosphatidylcholine, Bos taurus Reactome:REACT_111159 Partial proteolysis of antigen in phagolysosomes, Homo sapiens Reactome:REACT_15331 Hydrolysis of phosphatidylcholine, Homo sapiens Reactome:REACT_83734 Hydrolysis of phosphatidylcholine, Danio rerio Reactome:REACT_84047 Hydrolysis of phosphatidylcholine, Xenopus tropicalis Reactome:REACT_87959 Hydrolysis of phosphatidylcholine, Gallus gallus Reactome:REACT_88159 Hydrolysis of phosphatidylcholine, Canis familiaris Reactome:REACT_90118 Hydrolysis of phosphatidylcholine, Mus musculus Reactome:REACT_91045 Hydrolysis of phosphatidylcholine, Taeniopygia guttata Reactome:REACT_98572 Hydrolysis of phosphatidylcholine, Rattus norvegicus Catalysis of the hydrolysis of any ester bond. EC:3.1 Reactome:REACT_106563 Reactome:REACT_109748 Reactome:REACT_112177 Reactome:REACT_19294 Reactome:REACT_1978 Reactome:REACT_45174 Reactome:REACT_77112 Reactome:REACT_81282 Reactome:REACT_83347 Reactome:REACT_88228 Reactome:REACT_88314 Reactome:REACT_89615 Reactome:REACT_92446 Reactome:REACT_94475 esterase activity molecular_function GO:0016788 hydrolase activity, acting on ester bonds Catalysis of the hydrolysis of any ester bond. GOC:jl Reactome:REACT_106563 Deacylation of Acyl Ghrelin, Mus musculus Reactome:REACT_109748 Deacylation of Acyl Ghrelin, Bos taurus Reactome:REACT_112177 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Xenopus tropicalis Reactome:REACT_19294 Deacylation of Acyl Ghrelin, Homo sapiens Reactome:REACT_1978 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Homo sapiens Reactome:REACT_45174 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Mus musculus Reactome:REACT_77112 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Danio rerio Reactome:REACT_81282 Deacylation of Acyl Ghrelin, Rattus norvegicus Reactome:REACT_83347 Deacylation of Acyl Ghrelin, Gallus gallus Reactome:REACT_88228 Deacylation of Acyl Ghrelin, Canis familiaris Reactome:REACT_88314 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Sus scrofa Reactome:REACT_89615 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Rattus norvegicus Reactome:REACT_92446 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Canis familiaris Reactome:REACT_94475 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Bos taurus The targeting and directed movement of proteins into a cell or organelle. Not all import involves an initial targeting event. protein uptake biological_process GO:0017038 protein import The targeting and directed movement of proteins into a cell or organelle. Not all import involves an initial targeting event. GOC:ai The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle anabolism heterocycle biosynthesis heterocycle formation heterocycle synthesis biological_process GO:0018130 heterocycle biosynthetic process The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). ISBN:0198547684 Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0019219 regulation of nucleobase-containing compound metabolic process Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. regulation of metabolism biological_process GO:0019222 regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring. aromatic compound anabolism aromatic compound biosynthesis aromatic compound formation aromatic compound synthesis aromatic hydrocarbon biosynthesis aromatic hydrocarbon biosynthetic process biological_process GO:0019438 aromatic compound biosynthetic process The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring. GOC:ai The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. aromatic compound breakdown aromatic compound catabolism aromatic compound degradation aromatic hydrocarbon catabolic process aromatic hydrocarbon catabolism biological_process GO:0019439 aromatic compound catabolic process The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. GOC:ai The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. biological_process GO:0022402 cell cycle process The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. GOC:isa_complete GOC:mtg_cell_cycle One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. biological_process GO:0022403 cell cycle phase One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. GOC:mtg_cell_cycle A cellular process that results in the breakdown of a cellular component. GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process GO:0022411 cellular component disassembly A cellular process that results in the breakdown of a cellular component. GOC:isa_complete The aggregation, arrangement and bonding together of a cellular component. GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process GO:0022607 cellular component assembly The aggregation, arrangement and bonding together of a cellular component. GOC:isa_complete The attachment of a cell or organism to a substrate or other organism. biological_process GO:0022610 biological adhesion The attachment of a cell or organism to a substrate or other organism. GOC:isa_complete Any process that modulates the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process regulation of signaling process regulation of signalling process GO:0023051 regulation of signaling Any process that modulates the frequency, rate or extent of a signaling process. GOC:mtg_signal regulation of signaling process GOC:bf regulation of signalling process GOC:mah The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. 2010-02-16T09:30:50Z GO:0023046 biological signaling signaling process signalling biological_process signalling process GO:0023052 Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. signaling The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. GOC:mtg_signal GOC:mtg_signaling_feb11 GOC:signaling signalling process GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z positive regulation of signalling process biological_process positive regulation of signaling process GO:0023056 positive regulation of signaling Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. GOC:mtg_signal positive regulation of signalling process GOC:mah positive regulation of signaling process GOC:bf Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process negative regulation of signaling process negative regulation of signalling process GO:0023057 negative regulation of signaling Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. GOC:mtg_signal negative regulation of signaling process GOC:bf negative regulation of signalling process GOC:mah A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments. Wikipedia:Lamellipodia cellular_component GO:0030027 lamellipodium A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments. ISBN:0815316194 Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins. biological_process microfilament-based process GO:0030029 actin filament-based process Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. cell projection organisation biological_process cell projection organization and biogenesis cell surface structure organization and biogenesis GO:0030030 cell projection organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah http://www.cogsci.princeton.edu/~wn/ cell projection organisation GOC:curators cell projection organization and biogenesis GOC:mah cell surface structure organization and biogenesis GOC:mah Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. formation of a cell surface projection biological_process cell projection biogenesis GO:0030031 cell projection assembly Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah http://www.cogsci.princeton.edu/~wn/ cell projection biogenesis GOC:mah Movement of organelles or other particles along actin filaments, or sliding of actin filaments past each other, mediated by motor proteins. biological_process GO:0030048 actin filament-based movement Movement of organelles or other particles along actin filaments, or sliding of actin filaments past each other, mediated by motor proteins. GOC:BHF GOC:mah A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. Wikipedia:Cell_junction cellular_component GO:0030054 cell junction A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. GOC:mah ISBN:0198506732 http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html A cell junction that forms a connection between a cell and the extracellular matrix. cell-matrix junction cellular_component GO:0030055 cell-substrate junction A cell junction that forms a connection between a cell and the extracellular matrix. GOC:hb GOC:mah A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting. NIF_Subcellular:sao1362520468 endocytotic transport vesicle endocytotic vesicle cellular_component GO:0030139 endocytic vesicle A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting. GOC:go_curators PMID:19696797 The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. Wikipedia:Cellular_differentiation biological_process GO:0030154 cell differentiation The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. ISBN:0198506732 Thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft. GO:0030028 NIF_Subcellular:sao-1046371754 Wikipedia:Filopodia cellular_component GO:0030175 A filopodium may be approximately 0.1 um wide, 5-10 um long, and up to 50 um long in axon growth cones; may contain a loose bundle of about 20 actin filaments oriented with their plus ends pointing outward. Note that filopodia on dendritic shafts are distinct from other types of filopodia (even those found in dendritic growth cones) and may react differently to stimuli, as shown in PMID:12904473. filopodium Thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft. GOC:mah GOC:pr ISBN:0815316194 The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GO:0000068 DNA condensation eukaryotic chromosome condensation nuclear chromosome condensation biological_process GO:0030261 chromosome condensation The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GOC:mah ISBN:0815316194 DNA condensation Wikipedia:DNA_condensation eukaryotic chromosome condensation GOC:bf nuclear chromosome condensation GOC:bf Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis. apoptotic nuclear change biological_process GO:0030262 apoptotic nuclear changes Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis. GOC:mah GOC:mtg_apoptosis The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter. NIF_Subcellular:sao1770195789 Wikipedia:Axon cellular_component GO:0030424 axon The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter. GOC:nln ISBN:0198506732 A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. NIF_Subcellular:sao1211023249 Wikipedia:Dendrite cellular_component GO:0030425 dendrite A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. GOC:dos GOC:mah GOC:nln ISBN:0198506732 The portion of the cytoskeleton that lies just beneath the plasma membrane. cellular_component GO:0030863 cortical cytoskeleton The portion of the cytoskeleton that lies just beneath the plasma membrane. GOC:mah The portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane. cellular_component GO:0030864 cortical actin cytoskeleton The portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane. GOC:mah A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. intraflagellar transport complex intraflagellar transport particle cellular_component IFT complex GO:0030990 Note that we deem cilia and microtubule-based flagella to be equivalent. intraciliary transport particle A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. GOC:cilia GOC:kmv PMID:14570576 PMID:22118932 PMID:23945166 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microtubule organizing center, a structure from which microtubules grow. microtubule organising center organisation biological_process microtubule organizing center organization and biogenesis GO:0031023 microtubule organizing center organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microtubule organizing center, a structure from which microtubules grow. GOC:dph GOC:jl GOC:mah microtubule organising center organisation GOC:curators microtubule organizing center organization and biogenesis GOC:mah A membrane-bounded organelle of ciliated protozoan cells that contains a diploid copy of the cell's complete genome. Sections of contiguous sequence in the macronucleus are often interrupted by internal eliminated sequences (IES), and may be permuted, in micronuclei. Genic transcription is not found in micronuclei. Some ciliate species may contain multiple micronuclei per cell. Wikipedia:Micronucleus cellular_component GO:0031040 micronucleus A membrane-bounded organelle of ciliated protozoan cells that contains a diploid copy of the cell's complete genome. Sections of contiguous sequence in the macronucleus are often interrupted by internal eliminated sequences (IES), and may be permuted, in micronuclei. Genic transcription is not found in micronuclei. Some ciliate species may contain multiple micronuclei per cell. GOC:ns The area of a motile cell closest to the direction of movement. front of cell leading edge of cell cellular_component GO:0031252 cell leading edge The area of a motile cell closest to the direction of movement. GOC:pg Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. regulation of cellular metabolism biological_process GO:0031323 regulation of cellular metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. down regulation of cellular metabolic process down-regulation of cellular metabolic process downregulation of cellular metabolic process negative regulation of cellular metabolism inhibition of cellular metabolic process biological_process GO:0031324 negative regulation of cellular metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. Reactome:REACT_101225 Reactome:REACT_102187 Reactome:REACT_102331 Reactome:REACT_105293 Reactome:REACT_108571 Reactome:REACT_109170 Reactome:REACT_2122 Reactome:REACT_28360 Reactome:REACT_31270 Reactome:REACT_79603 Reactome:REACT_80902 Reactome:REACT_83058 Reactome:REACT_84314 Reactome:REACT_86633 Reactome:REACT_87840 Reactome:REACT_88060 Reactome:REACT_91293 Reactome:REACT_91429 Reactome:REACT_91906 Reactome:REACT_92487 Reactome:REACT_99393 positive regulation of cellular metabolism up regulation of cellular metabolic process up-regulation of cellular metabolic process upregulation of cellular metabolic process activation of cellular metabolic process stimulation of cellular metabolic process biological_process GO:0031325 positive regulation of cellular metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Reactome:REACT_101225 ChREBP activates metabolic gene expression, Mus musculus Reactome:REACT_102187 ChREBP activates metabolic gene expression, Escherichia coli Reactome:REACT_102331 ChREBP activates metabolic gene expression, Caenorhabditis elegans Reactome:REACT_105293 ChREBP activates metabolic gene expression, Plasmodium falciparum Reactome:REACT_108571 ChREBP activates metabolic gene expression, Drosophila melanogaster Reactome:REACT_109170 ChREBP activates metabolic gene expression, Xenopus tropicalis Reactome:REACT_2122 ChREBP activates metabolic gene expression, Homo sapiens Reactome:REACT_28360 ChREBP activates metabolic gene expression, Arabidopsis thaliana Reactome:REACT_31270 ChREBP activates metabolic gene expression, Mycobacterium tuberculosis Reactome:REACT_79603 ChREBP activates metabolic gene expression, Canis familiaris Reactome:REACT_80902 ChREBP activates metabolic gene expression, Saccharomyces cerevisiae Reactome:REACT_83058 ChREBP activates metabolic gene expression, Taeniopygia guttata Reactome:REACT_84314 ChREBP activates metabolic gene expression, Oryza sativa Reactome:REACT_86633 ChREBP activates metabolic gene expression, Dictyostelium discoideum Reactome:REACT_87840 ChREBP activates metabolic gene expression, Danio rerio Reactome:REACT_88060 ChREBP activates metabolic gene expression, Rattus norvegicus Reactome:REACT_91293 ChREBP activates metabolic gene expression, Staphylococcus aureus N315 Reactome:REACT_91429 ChREBP activates metabolic gene expression, Gallus gallus Reactome:REACT_91906 ChREBP activates metabolic gene expression, Schizosaccharomyces pombe Reactome:REACT_92487 ChREBP activates metabolic gene expression, Bos taurus Reactome:REACT_99393 ChREBP activates metabolic gene expression, Sus scrofa Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. regulation of cellular anabolism regulation of cellular biosynthesis regulation of cellular formation regulation of cellular synthesis biological_process GO:0031326 regulation of cellular biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. down regulation of cellular biosynthetic process down-regulation of cellular biosynthetic process downregulation of cellular biosynthetic process negative regulation of cellular anabolism negative regulation of cellular biosynthesis negative regulation of cellular formation negative regulation of cellular synthesis inhibition of cellular biosynthetic process biological_process GO:0031327 negative regulation of cellular biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. positive regulation of cellular anabolism positive regulation of cellular biosynthesis positive regulation of cellular formation positive regulation of cellular synthesis up regulation of cellular biosynthetic process up-regulation of cellular biosynthetic process upregulation of cellular biosynthetic process activation of cellular biosynthetic process stimulation of cellular biosynthetic process biological_process GO:0031328 positive regulation of cellular biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah A vesicle formed of membrane or protein, found in the cytoplasm of a cell. NIF_Subcellular:sao180601769 cellular_component GO:0031410 cytoplasmic vesicle A vesicle formed of membrane or protein, found in the cytoplasm of a cell. GOC:mah A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. establishment and maintenance of protein complex localization protein complex localisation biological_process GO:0031503 protein complex localization A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. GOC:mah protein complex localisation GOC:mah A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure. Polycomb Group protein complex cellular_component GO:0031519 PcG protein complex A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure. PMID:9372908 The attachment of a cell to the underlying substrate via adhesion molecules. biological_process GO:0031589 cell-substrate adhesion The attachment of a cell to the underlying substrate via adhesion molecules. GOC:mah GOC:pf The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen. cellular_component GO:0031974 membrane-enclosed lumen The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen. GOC:add GOC:mah The volume enclosed by the nuclear inner membrane. cellular_component GO:0031981 nuclear lumen The volume enclosed by the nuclear inner membrane. GOC:mah GOC:pz Any small, fluid-filled, spherical organelle enclosed by membrane or protein. NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component GO:0031982 vesicle Any small, fluid-filled, spherical organelle enclosed by membrane or protein. GOC:mah GOC:pz Any small, fluid-filled, spherical organelle enclosed by a lipid bilayer. membrane-enclosed vesicle cellular_component GO:0031988 membrane-bounded vesicle Any small, fluid-filled, spherical organelle enclosed by a lipid bilayer. GOC:mah The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses. blebbing membrane blebbing cell blebbing plasma membrane bleb assembly plasma membrane blebbing biological_process GO:0032060 bleb assembly The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses. GOC:mah GOC:mtg_apoptosis PMID:12083798 PMID:16624291 http://en.wikipedia.org/wiki/Bleb_(cell_biology) blebbing GOC:pr membrane blebbing GOC:pr plasma membrane bleb assembly GOC:pr plasma membrane blebbing GOC:pr Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB. inhibition of NF-kappaB transcription factor biological_process NF-kappaB inhibitor GO:0032088 negative regulation of NF-kappaB transcription factor activity Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB. GOC:dph GOC:rl GOC:tb inhibition of NF-kappaB transcription factor GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the directed movement of substances within cells. biological_process GO:0032386 regulation of intracellular transport Any process that modulates the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells. down regulation of intracellular transport down-regulation of intracellular transport downregulation of intracellular transport inhibition of intracellular transport biological_process GO:0032387 negative regulation of intracellular transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells. up regulation of intracellular transport up-regulation of intracellular transport upregulation of intracellular transport activation of intracellular transport stimulation of intracellular transport biological_process GO:0032388 positive regulation of intracellular transport Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells. GOC:mah An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. GO:0000141 GO:0030482 cellular_component actin cable GO:0032432 actin filament bundle An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. GOC:mah actin cable GOC:mah A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. development biological_process GO:0032502 developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. GOC:isa_complete Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere. biological_process maintenance of protein localization in cell GO:0032507 maintenance of protein location in cell Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere. GOC:isa_complete GOC:mah maintenance of protein localization in cell GOC:dph GOC:tb The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication. RNA anabolism RNA biosynthesis RNA formation RNA synthesis biological_process GO:0032774 Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study. RNA biosynthetic process The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication. GOC:mah GOC:txnOH Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. regulation of localisation biological_process GO:0032879 regulation of localization Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. GOC:mah regulation of localisation GOC:mah Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location. regulation of protein localisation biological_process GO:0032880 regulation of protein localization Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location. GOC:dph GOC:mah GOC:tb regulation of protein localisation GOC:mah The controlled release of a substance by a cell. Wikipedia:Secretion cellular secretion biological_process GO:0032940 secretion by cell The controlled release of a substance by a cell. GOC:mah The process in which cellular structures, including whole cells or cell parts, are generated and organized. cellular structure morphogenesis biological_process GO:0032989 cellular component morphogenesis The process in which cellular structures, including whole cells or cell parts, are generated and organized. GOC:dph GOC:mah GOC:tb cellular structure morphogenesis GOC:dph GOC:tb A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together. macromolecule complex cellular_component GO:0032991 macromolecular complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together. GOC:mah Any process in which a macromolecule is transported to, or maintained in, a specific location. macromolecule localisation biological_process GO:0033036 macromolecule localization Any process in which a macromolecule is transported to, or maintained in, a specific location. GOC:mah macromolecule localisation GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells. biological_process GO:0033157 regulation of intracellular protein transport Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells. GOC:mah A process in which a protein is transported to, or maintained in, a location within an organelle. protein localisation to organelle protein localization in organelle biological_process GO:0033365 protein localization to organelle A process in which a protein is transported to, or maintained in, a location within an organelle. GOC:mah protein localisation to organelle GOC:mah protein localization in organelle GOC:mah Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). biological_process GO:0033554 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to stress Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:mah Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group. Reactome:REACT_115680 Reactome:REACT_115778 Reactome:REACT_115899 Reactome:REACT_115932 Reactome:REACT_116106 Reactome:REACT_116167 DNA nucleotidyltransferase activity deoxynucleate polymerase activity deoxyribonucleate nucleotidyltransferase activity deoxyribonucleic acid polymerase activity deoxyribonucleic polymerase activity molecular_function GO:0034061 DNA polymerase activity Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group. EC:2.7.7.7 GOC:mah Reactome:REACT_115680 Insertion of correct bases opposite to the lesion by Pol kappa, Gallus gallus Reactome:REACT_115778 Elongation by Pol zeta complex, Gallus gallus Reactome:REACT_115899 Elongation by Pol kappa, Gallus gallus Reactome:REACT_115932 Insertion of correct bases opposite to the lesion by Pol eta, Gallus gallus Reactome:REACT_116106 Repair of ~27-30 bp long patch by DNA Pol Epsilon, Gallus gallus Reactome:REACT_116167 Elongation by Pol eta, Gallus gallus DNA nucleotidyltransferase activity EC:2.7.7.7 deoxynucleate polymerase activity EC:2.7.7.7 deoxyribonucleate nucleotidyltransferase activity EC:2.7.7.7 deoxyribonucleic acid polymerase activity EC:2.7.7.7 deoxyribonucleic polymerase activity EC:2.7.7.7 A process in which a protein is transported to, or maintained in, a location within the Golgi apparatus. protein localisation in Golgi apparatus protein localization in Golgi apparatus biological_process GO:0034067 protein localization to Golgi apparatus A process in which a protein is transported to, or maintained in, a location within the Golgi apparatus. GOC:mah protein localisation in Golgi apparatus GOC:mah protein localization in Golgi apparatus GOC:curators The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate. cell spreading during cell substrate adhesion substrate adhesion dependent cell spreading biological_process GO:0034446 substrate adhesion-dependent cell spreading The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate. GOC:mah GOC:pf PMID:17050732 A process in which a protein is transported to, or maintained in, a location within the nucleus. protein localisation to nucleus protein localization in cell nucleus protein localization in nucleus biological_process GO:0034504 protein localization to nucleus A process in which a protein is transported to, or maintained in, a location within the nucleus. GOC:ecd protein localisation to nucleus GOC:mah protein localization in nucleus GOC:mah Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GO:0016249 cellular protein localisation channel localizer activity biological_process GO:0034613 cellular protein localization Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GOC:mah cellular protein localisation GOC:mah channel localizer activity GOC:mah The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. Reactome:REACT_102000 Reactome:REACT_103710 Reactome:REACT_107293 Reactome:REACT_108179 Reactome:REACT_109042 Reactome:REACT_13 Reactome:REACT_28699 Reactome:REACT_29108 Reactome:REACT_32429 Reactome:REACT_33347 Reactome:REACT_34326 Reactome:REACT_55564 Reactome:REACT_77741 Reactome:REACT_82379 Reactome:REACT_86268 Reactome:REACT_90299 Reactome:REACT_91959 Reactome:REACT_93580 Reactome:REACT_95666 Reactome:REACT_98086 Reactome:REACT_99241 cellular nitrogen compound metabolism biological_process GO:0034641 cellular nitrogen compound metabolic process The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. GOC:mah Reactome:REACT_102000 Metabolism of amino acids and derivatives, Mycobacterium tuberculosis Reactome:REACT_103710 Metabolism of amino acids and derivatives, Escherichia coli Reactome:REACT_107293 Metabolism of amino acids and derivatives, Arabidopsis thaliana Reactome:REACT_108179 Metabolism of amino acids and derivatives, Xenopus tropicalis Reactome:REACT_109042 Metabolism of amino acids and derivatives, Sus scrofa Reactome:REACT_13 Metabolism of amino acids and derivatives, Homo sapiens Reactome:REACT_28699 Metabolism of amino acids and derivatives, Saccharomyces cerevisiae Reactome:REACT_29108 Metabolism of amino acids and derivatives, Caenorhabditis elegans Reactome:REACT_32429 Metabolism of amino acids and derivatives, Rattus norvegicus Reactome:REACT_33347 Metabolism of amino acids and derivatives, Mus musculus Reactome:REACT_34326 Metabolism of amino acids and derivatives, Staphylococcus aureus N315 Reactome:REACT_55564 Metabolism of amino acids and derivatives, Gallus gallus Reactome:REACT_77741 Metabolism of amino acids and derivatives, Taeniopygia guttata Reactome:REACT_82379 Metabolism of amino acids and derivatives, Bos taurus Reactome:REACT_86268 Metabolism of amino acids and derivatives, Drosophila melanogaster Reactome:REACT_90299 Metabolism of amino acids and derivatives, Oryza sativa Reactome:REACT_91959 Metabolism of amino acids and derivatives, Plasmodium falciparum Reactome:REACT_93580 Metabolism of amino acids and derivatives, Danio rerio Reactome:REACT_95666 Metabolism of amino acids and derivatives, Canis familiaris Reactome:REACT_98086 Metabolism of amino acids and derivatives, Dictyostelium discoideum Reactome:REACT_99241 Metabolism of amino acids and derivatives, Schizosaccharomyces pombe The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells. GO:0034961 cellular biopolymer biosynthetic process cellular macromolecule anabolism cellular macromolecule biosynthesis cellular macromolecule formation cellular macromolecule synthesis biological_process GO:0034645 cellular macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells. CHEBI:33694 GOC:mah cellular biopolymer biosynthetic process GOC:mtg_chebi_dec09 cellular macromolecule anabolism GOC:mah cellular macromolecule biosynthesis GOC:mah cellular macromolecule formation GOC:mah cellular macromolecule synthesis GOC:mah The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids. nucleobase, nucleoside, nucleotide and nucleic acid anabolism nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis nucleobase, nucleoside, nucleotide and nucleic acid formation nucleobase, nucleoside, nucleotide and nucleic acid synthesis biological_process GO:0034654 nucleobase-containing compound biosynthetic process The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids. GOC:mah The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. nucleobase, nucleoside, nucleotide and nucleic acid breakdown nucleobase, nucleoside, nucleotide and nucleic acid catabolism nucleobase, nucleoside, nucleotide and nucleic acid degradation biological_process nucleobase, nucleoside, nucleotide and nucleic acid catabolic process GO:0034655 nucleobase-containing compound catabolic process The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. GOC:mah nucleobase, nucleoside, nucleotide and nucleic acid catabolic process GOC:dph GOC:tb A process in which a protein is transported to, or maintained at, a microtubule. rfoulger 2010-03-11T11:00:56Z protein localisation to microtubule biological_process GO:0035372 protein localization to microtubule A process in which a protein is transported to, or maintained at, a microtubule. GOC:bf GOC:lb protein localisation to microtubule GOC:mah The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. rfoulger 2010-05-14T01:14:37Z GO:0007242 GO:0007243 GO:0023013 GO:0023034 Reactome:REACT_100795 Reactome:REACT_102462 Reactome:REACT_104200 Reactome:REACT_108216 Reactome:REACT_1525 Reactome:REACT_80030 Reactome:REACT_83068 Reactome:REACT_83869 Reactome:REACT_87453 Reactome:REACT_89085 Reactome:REACT_89983 Reactome:REACT_90740 Reactome:REACT_99938 intracellular signaling chain intracellular protein kinase cascade intracellular signal transduction pathway protein kinase cascade signal transmission via intracellular cascade biological_process intracellular signaling cascade intracellular signaling pathway signal transduction via intracellular signaling cascade GO:0035556 intracellular signal transduction The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. GOC:bf GOC:jl GOC:signaling ISBN:3527303782 Reactome:REACT_100795 PKA-mediated phosphorylation of key metabolic factors, Saccharomyces cerevisiae Reactome:REACT_102462 PKA-mediated phosphorylation of key metabolic factors, Canis familiaris Reactome:REACT_104200 PKA-mediated phosphorylation of key metabolic factors, Taeniopygia guttata Reactome:REACT_108216 PKA-mediated phosphorylation of key metabolic factors, Dictyostelium discoideum Reactome:REACT_1525 PKA-mediated phosphorylation of key metabolic factors, Homo sapiens Reactome:REACT_80030 PKA-mediated phosphorylation of key metabolic factors, Sus scrofa Reactome:REACT_83068 PKA-mediated phosphorylation of key metabolic factors, Gallus gallus Reactome:REACT_83869 PKA-mediated phosphorylation of key metabolic factors, Xenopus tropicalis Reactome:REACT_87453 PKA-mediated phosphorylation of key metabolic factors, Bos taurus Reactome:REACT_89085 PKA-mediated phosphorylation of key metabolic factors, Rattus norvegicus Reactome:REACT_89983 PKA-mediated phosphorylation of key metabolic factors, Danio rerio Reactome:REACT_90740 PKA-mediated phosphorylation of key metabolic factors, Schizosaccharomyces pombe Reactome:REACT_99938 PKA-mediated phosphorylation of key metabolic factors, Mus musculus intracellular signaling chain ISBN:3527303782 intracellular protein kinase cascade GOC:signaling protein kinase cascade GOC:signaling intracellular signaling cascade GOC:signaling A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix. rfoulger 2011-05-17T03:04:42Z site of DSB cellular_component DNA damage foci DNA damage focus IRIF ionizing radiation-induced foci GO:0035861 site of double-strand break A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix. GOC:bf GOC:mah GOC:vw PMID:20096808 PMID:21035408 site of DSB PMID:21035408 DNA damage foci GOC:vw DNA damage focus GOC:mah PMID:20096808 PMID:21035408 IRIF PMID:20096808 PMID:21035408 ionizing radiation-induced foci PMID:20096808 PMID:21035408 The region of a neuron that includes the cell body (cell soma) and the dendrite, but excludes the axon. rebeccafoulger 2014-07-24T10:06:19Z cellular_component GO:0036477 somatodendritic compartment The region of a neuron that includes the cell body (cell soma) and the dendrite, but excludes the axon. GOC:PARL GOC:pad The increase in size or mass of an entire organism, a part of an organism or a cell. GO:0048590 biological_process growth pattern non-developmental growth GO:0040007 See also the biological process term 'cell growth ; GO:0016049'. growth The increase in size or mass of an entire organism, a part of an organism or a cell. GOC:bf GOC:ma non-developmental growth GOC:mah Self-propelled movement of a cell or organism from one location to another. biological_process GO:0040011 locomotion Self-propelled movement of a cell or organism from one location to another. GOC:dgh Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. response to chemical stimulus response to chemical substance biological_process GO:0042221 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to chemical Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. GOC:jl response to chemical stimulus GOC:dos Any process that modulates the frequency, rate or extent of movement of proteins from the cytoplasm to the nucleus. regulation of protein import into cell nucleus regulation of protein transport from cytoplasm to nucleus regulation of protein-nucleus import biological_process GO:0042306 regulation of protein import into nucleus Any process that modulates the frequency, rate or extent of movement of proteins from the cytoplasm to the nucleus. GOC:jl Any process that activates or increases the frequency, rate or extent of movement of proteins from the cytoplasm into the nucleus. positive regulation of protein import into cell nucleus positive regulation of protein transport from cytoplasm to nucleus positive regulation of protein-nucleus import up regulation of protein import into nucleus up-regulation of protein import into nucleus upregulation of protein import into nucleus activation of protein import into nucleus stimulation of protein import into nucleus biological_process GO:0042307 positive regulation of protein import into nucleus Any process that activates or increases the frequency, rate or extent of movement of proteins from the cytoplasm into the nucleus. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of proteins from the cytoplasm into the nucleus. down regulation of protein import into nucleus down-regulation of protein import into nucleus downregulation of protein import into nucleus negative regulation of protein import into cell nucleus negative regulation of protein transport from cytoplasm to nucleus negative regulation of protein-nucleus import inhibition of protein import into nucleus biological_process GO:0042308 negative regulation of protein import into nucleus Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of proteins from the cytoplasm into the nucleus. GOC:jl Any process that modulates the frequency, rate or extent of the transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane. regulation of NF-kappaB import into cell nucleus regulation of NF-kappaB transport from cytoplasm to nucleus regulation of NF-kappaB-nucleus import biological_process GO:0042345 regulation of NF-kappaB import into nucleus Any process that modulates the frequency, rate or extent of the transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane. GOC:jl ISBN:0198506732 Any process that activates or increases the frequency, rate or extent of transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane. positive regulation of NF-kappaB import into cell nucleus positive regulation of NF-kappaB transport from cytoplasm to nucleus positive regulation of NF-kappaB-nucleus import up regulation of NF-kappaB import into nucleus up-regulation of NF-kappaB import into nucleus upregulation of NF-kappaB import into nucleus activation of NF-kappaB import into nucleus stimulation of NF-kappaB import into nucleus biological_process GO:0042346 positive regulation of NF-kappaB import into nucleus Any process that activates or increases the frequency, rate or extent of transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane. GOC:jl ISBN:0198506732 Any process that stops, prevents, or reduces the frequency, rate or extent of the transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane. down regulation of NF-kappaB import into nucleus down-regulation of NF-kappaB import into nucleus downregulation of NF-kappaB import into nucleus negative regulation of NF-kappaB import into cell nucleus negative regulation of NF-kappaB transport from cytoplasm to nucleus negative regulation of NF-kappaB-nucleus import inhibition of NF-kappaB import into nucleus biological_process GO:0042347 negative regulation of NF-kappaB import into nucleus Any process that stops, prevents, or reduces the frequency, rate or extent of the transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane. GOC:jl ISBN:0198506732 The directed movement of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane. NF-KB import into nucleus NF-kappaB import into cell nucleus NF-kappaB protein-nucleus import NF-kappaB transport from cytoplasm to nucleus NF-kappaB-nucleus import biological_process GO:0042348 NF-kappaB import into nucleus The directed movement of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane. GOC:jl ISBN:0198506732 NF-KB import into nucleus GOC:bf Discrete subnuclear bodies in the interchromatin nucleoplasmic space, often located adjacent to nuclear specks. 10-20 paraspeckles are typically found in human cell nuclei. Wikipedia:Paraspeckle cellular_component GO:0042382 paraspeckles Discrete subnuclear bodies in the interchromatin nucleoplasmic space, often located adjacent to nuclear specks. 10-20 paraspeckles are typically found in human cell nuclei. GOC:jl PMID:11790299 Any complex of actin, myosin, and accessory proteins. actomyosin complex actomyosin structure cellular_component GO:0042641 actomyosin Any complex of actin, myosin, and accessory proteins. GOC:go_curators Polarized growth from one end of a cell. monopolar growth monopolar cell elongation polar cell elongation biological_process GO:0042814 monopolar cell growth Polarized growth from one end of a cell. GOC:vw The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0042886 amide transport The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl ISBN:0198506732 Any process that modulates the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus. regulation of transcription factor import into cell nucleus regulation of transcription factor transport from cytoplasm to nucleus regulation of transcription factor-nucleus import biological_process GO:0042990 regulation of transcription factor import into nucleus Any process that modulates the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus. GOC:jl The directed movement of a transcription factor from the cytoplasm to the nucleus. transcription factor import into cell nucleus transcription factor transport from cytoplasm to nucleus transcription factor-nucleus import biological_process GO:0042991 transcription factor import into nucleus The directed movement of a transcription factor from the cytoplasm to the nucleus. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus. down regulation of transcription factor import into nucleus down-regulation of transcription factor import into nucleus downregulation of transcription factor import into nucleus negative regulation of transcription factor import into cell nucleus negative regulation of transcription factor transport from cytoplasm to nucleus negative regulation of transcription factor-nucleus import inhibition of transcription factor import into nucleus biological_process GO:0042992 negative regulation of transcription factor import into nucleus Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus. GOC:jl Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus. positive regulation of transcription factor import into cell nucleus positive regulation of transcription factor transport from cytoplasm to nucleus positive regulation of transcription factor-nucleus import up regulation of transcription factor import into nucleus up-regulation of transcription factor import into nucleus upregulation of transcription factor import into nucleus activation of transcription factor import into nucleus stimulation of transcription factor import into nucleus biological_process GO:0042993 positive regulation of transcription factor import into nucleus Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus. GOC:jl The selective interaction of a transcription factor with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus. cytoplasmic retention of transcription factor cytoplasmic sequestration of transcription factor cytoplasmic storage of transcription factor maintenance of transcription factor protein location in cytoplasm retention of transcription factor in cytoplasm sequestering of transcription factor in cytoplasm sequestration of transcription factor in cytoplasm storage of transcription factor in cytoplasm transcription factor binding, cytoplasmic sequestering biological_process GO:0042994 cytoplasmic sequestering of transcription factor The selective interaction of a transcription factor with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus. GOC:jl maintenance of transcription factor protein location in cytoplasm GOC:dph GOC:tb A prolongation or process extending from a cell, e.g. a flagellum or axon. cell process cellular process cellular projection cellular_component GO:0042995 cell projection A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl http://www.cogsci.princeton.edu/~wn/ A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. NIF_Subcellular:sao-867568886 neuron process neuron protrusion neuronal cell projection neurite cellular_component GO:0043005 neuron projection A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. GOC:jl http://www.cogsci.princeton.edu/~wn/ neuron protrusion NIF_Subcellular:sao-250931889 Any process that modulates I-kappaB kinase/NF-kappaB signaling. biological_process regulation of I-kappaB kinase/NF-kappaB cascade GO:0043122 regulation of I-kappaB kinase/NF-kappaB signaling Any process that modulates I-kappaB kinase/NF-kappaB signaling. GOC:jl PMID:12773372 regulation of I-kappaB kinase/NF-kappaB cascade GOC:signaling Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling. Reactome:REACT_24918 stimulation of I-kappaB kinase/NF-kappaB cascade biological_process activation of I-kappaB kinase/NF-kappaB cascade positive regulation of I-kappaB kinase/NF-kappaB cascade up regulation of I-kappaB kinase/NF-kappaB cascade up-regulation of I-kappaB kinase/NF-kappaB cascade upregulation of I-kappaB kinase/NF-kappaB cascade GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling. GOC:jl Reactome:REACT_24918 IRAK1 recruits IKK complex, Homo sapiens positive regulation of I-kappaB kinase/NF-kappaB cascade GOC:signaling Any process that stops, prevents, or reduces the frequency, rate or extent of -kappaB kinase/NF-kappaB signaling. inhibition of I-kappaB kinase/NF-kappaB cascade biological_process down regulation of I-kappaB kinase/NF-kappaB cascade down-regulation of I-kappaB kinase/NF-kappaB cascade downregulation of I-kappaB kinase/NF-kappaB cascade negative regulation of I-kappaB kinase/NF-kappaB cascade GO:0043124 negative regulation of I-kappaB kinase/NF-kappaB signaling Any process that stops, prevents, or reduces the frequency, rate or extent of -kappaB kinase/NF-kappaB signaling. GOC:jl negative regulation of I-kappaB kinase/NF-kappaB cascade GOC:signaling The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0043283 biopolymer metabolic process macromolecule metabolism biological_process GO:0043170 macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. CHEBI:33694 GOC:mah biopolymer metabolic process GOC:mtg_chebi_dec09 Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. NIF_Subcellular:sao1539965131 Wikipedia:Organelle cellular_component GO:0043226 organelle Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component GO:0043228 non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. GOC:go_curators Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. cellular_component GO:0043229 intracellular organelle Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. intracellular membrane-enclosed organelle cellular_component GO:0043231 intracellular membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. intracellular non-membrane-enclosed organelle cellular_component GO:0043232 intracellular non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. GOC:go_curators The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. cellular_component GO:0043233 organelle lumen The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. GOC:jl GOC:mah A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. Wikipedia:Protein_complex protein-protein complex cellular_component GO:0043234 A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. protein complex A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. GOC:go_curators http://www.ebi.ac.uk/intact/complex/documentation/ Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription. negative regulation of transcription factor activity down regulation of transcription factor activity down-regulation of transcription factor activity downregulation of transcription factor activity inhibition of transcription factor activity biological_process GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription. GOC:jl negative regulation of transcription factor activity GOC:dph GOC:tb Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. sequence specific DNA binding molecular_function GO:0043565 sequence-specific DNA binding Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. GOC:jl A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 cellular component biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. GOC:jl GOC:mah Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jane 2009-04-21T04:07:27Z biological_process GO:0044092 negative regulation of molecular function Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jane 2009-04-21T04:11:06Z biological_process GO:0044093 positive regulation of molecular function Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. jane 2009-11-04T12:58:25Z molecular_function GO:0044212 The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". transcription regulatory region DNA binding Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. GOC:jl GOC:txnOH SO:0005836 The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism biological_process intermediary metabolism GO:0044237 cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. GOC:go_curators intermediary metabolism GOC:mah The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. primary metabolism biological_process GO:0044238 primary metabolic process The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. GOC:go_curators http://www.metacyc.org The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. cellular breakdown cellular catabolism cellular degradation biological_process GO:0044248 cellular catabolic process The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:jl The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. cellular anabolism cellular biosynthesis cellular formation cellular synthesis biological_process GO:0044249 cellular biosynthetic process The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:jl The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells. GO:0034960 cellular biopolymer metabolic process cellular macromolecule metabolism biological_process GO:0044260 cellular macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells. CHEBI:33694 GOC:mah cellular biopolymer metabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells. GO:0034962 cellular biopolymer catabolic process cellular macromolecule breakdown cellular macromolecule catabolism cellular macromolecule degradation biological_process GO:0044265 cellular macromolecule catabolic process The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells. CHEBI:33694 GOC:jl cellular biopolymer catabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. nitrogen compound breakdown nitrogen compound catabolism nitrogen compound degradation biological_process GO:0044270 cellular nitrogen compound catabolic process The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. nitrogen compound anabolism nitrogen compound biosynthesis nitrogen compound formation nitrogen compound synthesis biological_process GO:0044271 cellular nitrogen compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. GOC:jl ISBN:0198506732 A dendrite arising from another dendrite. jane 2010-02-05T04:18:53Z NIF_Subcellular:sao884265541 dendrite branch cellular_component GO:0044307 dendritic branch A dendrite arising from another dendrite. NIF_Subcellular:sao884265541 A process in which a protein is transported to, or maintained in, a location within the cytoskeleton. janelomax 2011-12-13T11:43:24Z protein localisation to cytoskeleton biological_process GO:0044380 protein localization to cytoskeleton A process in which a protein is transported to, or maintained in, a location within the cytoskeleton. GOC:jl protein localisation to cytoskeleton GOC:mah Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane. cellular_component GO:0044422 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. organelle part Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane. GOC:jl Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. cellular_component GO:0044424 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. intracellular part Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. GOC:jl Any constituent part of a chromosome, a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. chromosomal component chromosome component chromosome part cellular_component GO:0044427 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. chromosomal part Any constituent part of a chromosome, a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. GOC:jl Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. NIF_Subcellular:sao1499850686 nuclear subcomponent nucleus component cellular_component GO:0044428 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. nuclear part Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. GOC:jl nuclear subcomponent NIF_Subcellular:sao1499850686 Any constituent part of a mitochondrion, a semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. NIF_Subcellular:sao666410040 mitochondrial subcomponent mitochondrion component cellular_component GO:0044429 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. mitochondrial part Any constituent part of a mitochondrion, a semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. GOC:jl mitochondrial subcomponent NIF_Subcellular:sao666410040 Any constituent part of the cytoskeleton, a cellular scaffolding or skeleton that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (e.g. the movement of vesicles and organelles) and cellular division. Includes constituent parts of intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice. NIF_Subcellular:sao1635329413 cytoskeletal element cytoskeleton component cellular_component GO:0044430 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cytoskeletal part Any constituent part of the cytoskeleton, a cellular scaffolding or skeleton that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (e.g. the movement of vesicles and organelles) and cellular division. Includes constituent parts of intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice. GOC:jl cytoskeletal element NIF_Subcellular:sao1635329413 Any constituent part of the Golgi apparatus, a compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. NIF_Subcellular:sao624292949 Golgi component Golgi subcomponent cellular_component GO:0044431 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. Golgi apparatus part Any constituent part of the Golgi apparatus, a compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. GOC:jl Golgi subcomponent NIF_Subcellular:sao624292949 Any constituent part of the endoplasmic reticulum, the irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. ER component cellular_component GO:0044432 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. endoplasmic reticulum part Any constituent part of the endoplasmic reticulum, the irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. GOC:jl Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. cytoplasm component cellular_component GO:0044444 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cytoplasmic part Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GOC:jl A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane. cellular_component GO:0044446 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. intracellular organelle part A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane. GOC:jl Any constituent part of the cell cortex, the region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. cellular_component GO:0044448 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cell cortex part Any constituent part of the cell cortex, the region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. GOC:jl Any constituent part of the nucleoplasm, that part of the nuclear content other than the chromosomes or the nucleolus. cellular_component GO:0044451 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. nucleoplasm part Any constituent part of the nucleoplasm, that part of the nuclear content other than the chromosomes or the nucleolus. GOC:jl Any constituent part of a cell projection, a prolongation or process extending from a cell, e.g. a flagellum or axon. cellular_component GO:0044463 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cell projection part Any constituent part of a cell projection, a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl Any constituent part of a cell, the basic structural and functional unit of all organisms. NIF_Subcellular:sao628508602 cellular subcomponent cellular_component protoplast GO:0044464 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cell part Any constituent part of a cell, the basic structural and functional unit of all organisms. GOC:jl cellular subcomponent NIF_Subcellular:sao628508602 protoplast GOC:mah A biological process that involves only one organism. janelomax 2012-09-19T15:05:24Z single organism process biological_process GO:0044699 single-organism process A biological process that involves only one organism. GOC:jl A signaling process occurring within a single organism. janelomax 2012-09-19T15:12:49Z biological_process GO:0044700 single organism signaling A signaling process occurring within a single organism. GOC:jl The process of directing proteins towards the nucleus, usually using signals contained within the protein. janelomax 2012-11-07T15:45:54Z biological_process GO:0044744 protein targeting to nucleus The process of directing proteins towards the nucleus, usually using signals contained within the protein. GOC:jl Any process that is carried out at the cellular level, occurring within a single organism. janelomax 2012-12-11T16:56:55Z biological_process GO:0044763 single-organism cellular process Any process that is carried out at the cellular level, occurring within a single organism. GOC:jl The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving a single organism. janelomax 2012-12-13T16:25:32Z biological_process GO:0044765 single-organism transport The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving a single organism. GOC:jl A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism. janelomax 2012-12-19T12:21:31Z biological_process GO:0044767 single-organism developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism. GOC:jl The cell cycle process by which a cell commits to entering the next cell cycle phase. janelomax 2013-02-28T12:54:59Z cell cycle transition biological_process GO:0044770 cell cycle phase transition The cell cycle process by which a cell commits to entering the next cell cycle phase. GOC:mtg_cell_cycle The cell cycle process by which a cell commits to entering the next mitotic cell cycle phase. janelomax 2013-02-28T13:09:33Z biological_process GO:0044772 mitotic cell cycle phase transition The cell cycle process by which a cell commits to entering the next mitotic cell cycle phase. GOC:mtg_cell_cycle The membrane organization process that joins two lipid bilayers to form a single membrane, involving only one organism. janelomax 2013-09-10T15:08:20Z biological_process GO:0044801 single-organism membrane fusion The membrane organization process that joins two lipid bilayers to form a single membrane, involving only one organism. GOC:jl A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane, involving only one organism. janelomax 2013-09-10T15:11:17Z biological_process GO:0044802 single-organism membrane organization A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane, involving only one organism. GOC:jl The cell cycle process by which a cell in G2 phase commits to M phase. janelomax 2014-03-05T14:56:45Z biological_process GO:0044839 cell cycle G2/M phase transition The cell cycle process by which a cell in G2 phase commits to M phase. GOC:jl GOC:mtg_cell_cycle A distinct period or stage in a biological process or cycle. janelomax 2014-07-16T13:12:40Z biological_process GO:0044848 Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase. biological phase A distinct period or stage in a biological process or cycle. GOC:jl The mitotic cell cycle phase transition whose occurrence commits the cell from the G0 quiescent state to the G1 phase. Under certain conditions, cells exit the cell cycle during G1 and remain in the G0 state as nongrowing, non-dividing (quiescent) cells. Appropriate stimulation of such cells induces them to return to G1 and resume growth and division. The G0 to G1 transition is accompanied by many changes in the program of gene expression. biological_process GO:0045023 G0 to G1 transition The mitotic cell cycle phase transition whose occurrence commits the cell from the G0 quiescent state to the G1 phase. Under certain conditions, cells exit the cell cycle during G1 and remain in the G0 state as nongrowing, non-dividing (quiescent) cells. Appropriate stimulation of such cells induces them to return to G1 and resume growth and division. The G0 to G1 transition is accompanied by many changes in the program of gene expression. GOC:mtg_cell_cycle ISBN:0716731363 The joining of two or more lipid bilayer membranes that surround a cell. GO:0006947 cell fusion cell-cell fusion biological_process GO:0045026 plasma membrane fusion The joining of two or more lipid bilayer membranes that surround a cell. GOC:elh GOC:mtg_muscle The directed movement of a protein to a specific location. establishment of protein localisation protein positioning protein recruitment biological_process GO:0045184 establishment of protein localization The directed movement of a protein to a specific location. GOC:bf establishment of protein localisation GOC:mah Any process in which a protein is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of proteins that do move away. active protein retrieval protein retention protein sequestering biological_process maintenance of protein localization GO:0045185 maintenance of protein location Any process in which a protein is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of proteins that do move away. GOC:bf maintenance of protein localization GOC:dph GOC:tb A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis. Wikipedia:Phagosome phagosome cellular_component GO:0045335 phagocytic vesicle A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis. GOC:go_curators ISBN:0198506732 Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. GO:0016481 GO:0032582 GO:0061021 down regulation of transcription, DNA-dependent down-regulation of transcription, DNA-dependent downregulation of transcription, DNA-dependent negative regulation of cellular transcription, DNA-dependent negative regulation of transcription, DNA-dependent inhibition of transcription, DNA-dependent biological_process down regulation of gene-specific transcription down-regulation of gene-specific transcription downregulation of gene-specific transcription inhibition of gene-specific transcription negative regulation of gene-specific transcription transcription repressor activity GO:0045892 negative regulation of transcription, DNA-templated Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. GOC:go_curators GOC:txnOH negative regulation of transcription, DNA-dependent GOC:txnOH Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. GO:0043193 GO:0045941 GO:0061020 positive regulation of cellular transcription, DNA-dependent positive regulation of transcription, DNA-dependent up regulation of transcription, DNA-dependent up-regulation of transcription, DNA-dependent upregulation of transcription, DNA-dependent activation of transcription, DNA-dependent stimulation of gene-specific transcription stimulation of transcription, DNA-dependent biological_process activation of gene-specific transcription positive regulation of gene-specific transcription transcription activator activity up regulation of gene-specific transcription up-regulation of gene-specific transcription upregulation of gene-specific transcription GO:0045893 positive regulation of transcription, DNA-templated Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. GOC:go_curators GOC:txnOH positive regulation of transcription, DNA-dependent GOC:txnOH Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism inhibition of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process biological_process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0045934 negative regulation of nucleobase-containing compound metabolic process Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process biological_process positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0045935 positive regulation of nucleobase-containing compound metabolic process Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle metabolism biological_process GO:0046483 heterocycle metabolic process The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). CHEBI:5686 ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle breakdown heterocycle catabolism heterocycle degradation biological_process GO:0046700 heterocycle catabolic process The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm. biological_process GO:0046822 regulation of nucleocytoplasmic transport Any process that modulates the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm. GOC:bf Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances between the cytoplasm and the nucleus. down regulation of nucleocytoplasmic transport down-regulation of nucleocytoplasmic transport downregulation of nucleocytoplasmic transport inhibition of nucleocytoplasmic transport biological_process GO:0046823 negative regulation of nucleocytoplasmic transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances between the cytoplasm and the nucleus. GOC:bf Any process that activates or increases the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm. up regulation of nucleocytoplasmic transport up-regulation of nucleocytoplasmic transport upregulation of nucleocytoplasmic transport activation of nucleocytoplasmic transport stimulation of nucleocytoplasmic transport biological_process GO:0046824 positive regulation of nucleocytoplasmic transport Any process that activates or increases the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm. GOC:bf The controlled release of a substance by a cell or a tissue. biological_process GO:0046903 secretion The controlled release of a substance by a cell or a tissue. GOC:ai The directed movement of substances within a cell. biological_process GO:0046907 intracellular transport The directed movement of substances within a cell. GOC:ai The creation of two or more organelles by division of one organelle. biological_process GO:0048285 organelle fission The creation of two or more organelles by division of one organelle. GOC:jid The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process terminal differentiation GO:0048468 cell development The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:go_curators terminal differentiation GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0043119 positive regulation of physiological process up regulation of biological process up-regulation of biological process upregulation of biological process activation of biological process stimulation of biological process biological_process GO:0048518 positive regulation of biological process Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0043118 down regulation of biological process down-regulation of biological process downregulation of biological process negative regulation of physiological process inhibition of biological process biological_process GO:0048519 negative regulation of biological process Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051242 positive regulation of cellular physiological process up regulation of cellular process up-regulation of cellular process upregulation of cellular process activation of cellular process stimulation of cellular process biological_process GO:0048522 positive regulation of cellular process Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051243 down regulation of cellular process down-regulation of cellular process downregulation of cellular process negative regulation of cellular physiological process inhibition of cellular process biological_process GO:0048523 negative regulation of cellular process Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. biological_process GO:0048583 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to stimulus Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. up regulation of response to stimulus up-regulation of response to stimulus upregulation of response to stimulus activation of response to stimulus stimulation of response to stimulus biological_process GO:0048584 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. positive regulation of response to stimulus Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. down regulation of response to stimulus down-regulation of response to stimulus downregulation of response to stimulus inhibition of response to stimulus biological_process GO:0048585 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. negative regulation of response to stimulus Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another. biological_process GO:0048589 developmental growth The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another. GOC:go_curators The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. development of an anatomical structure biological_process GO:0048856 This term was added by GO_REF:0000021. anatomical structure development The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GOC:mtg_15jun06 GO_REF:0000021 A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. biological_process GO:0048869 cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. GOC:isa_complete Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. cell locomotion movement of a cell biological_process cell movement GO:0048870 cell motility Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. GOC:dgh GOC:dph GOC:isa_complete GOC:mlg Any process in which a chromosome is transported to, or maintained in, a specific location. chromosome localisation establishment and maintenance of chromosome localization establishment and maintenance of chromosome position biological_process GO:0050000 chromosome localization Any process in which a chromosome is transported to, or maintained in, a specific location. GOC:ai chromosome localisation GOC:mah Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0050791 regulation of physiological process biological_process GO:0050789 regulation of biological process Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:ai GOC:go_curators Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051244 regulation of cellular physiological process biological_process GO:0050794 regulation of cellular process Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GO:0051869 physiological response to stimulus biological_process GO:0050896 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GOC:ai GOC:bf Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051049 regulation of transport Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of transport up-regulation of transport upregulation of transport activation of transport stimulation of transport biological_process GO:0051050 positive regulation of transport Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of transport down-regulation of transport downregulation of transport inhibition of transport biological_process GO:0051051 negative regulation of transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription. regulation of transcription factor activity Reactome:REACT_104536 Reactome:REACT_107559 Reactome:REACT_109535 Reactome:REACT_110257 Reactome:REACT_110693 Reactome:REACT_21326 Reactome:REACT_82719 Reactome:REACT_83365 Reactome:REACT_90659 Reactome:REACT_92725 Reactome:REACT_96476 Reactome:REACT_99415 biological_process GO:0051090 regulation of sequence-specific DNA binding transcription factor activity Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription. GOC:ai regulation of transcription factor activity GOC:dph GOC:tb Reactome:REACT_104536 Activation of the AP-1 family of transcription factors, Bos taurus Reactome:REACT_107559 Activation of the AP-1 family of transcription factors, Danio rerio Reactome:REACT_109535 Activation of the AP-1 family of transcription factors, Schizosaccharomyces pombe Reactome:REACT_110257 Activation of the AP-1 family of transcription factors, Drosophila melanogaster Reactome:REACT_110693 Activation of the AP-1 family of transcription factors, Gallus gallus Reactome:REACT_21326 Activation of the AP-1 family of transcription factors, Homo sapiens Reactome:REACT_82719 Activation of the AP-1 family of transcription factors, Xenopus tropicalis Reactome:REACT_83365 Activation of the AP-1 family of transcription factors, Sus scrofa Reactome:REACT_90659 Activation of the AP-1 family of transcription factors, Taeniopygia guttata Reactome:REACT_92725 Activation of the AP-1 family of transcription factors, Canis familiaris Reactome:REACT_96476 Activation of the AP-1 family of transcription factors, Rattus norvegicus Reactome:REACT_99415 Activation of the AP-1 family of transcription factors, Mus musculus Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription. positive regulation of transcription factor activity up regulation of transcription factor activity up-regulation of transcription factor activity upregulation of transcription factor activity activation of transcription factor activity stimulation of transcription factor activity biological_process GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription. GOC:ai positive regulation of transcription factor activity GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB. Reactome:REACT_107873 Reactome:REACT_113398 Reactome:REACT_113766 Reactome:REACT_21281 Reactome:REACT_31084 Reactome:REACT_33907 Reactome:REACT_34168 Reactome:REACT_34256 Reactome:REACT_87914 Reactome:REACT_95400 NF-kappaB activation activation of NF-kappaB activation of NF-kappaB transcription factor biological_process GO:0051092 positive regulation of NF-kappaB transcription factor activity Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB. GOC:dph GOC:tb PMID:15087454 PMID:15170030 Reactome:REACT_107873 TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Rattus norvegicus Reactome:REACT_113398 TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Taeniopygia guttata Reactome:REACT_113766 TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Drosophila melanogaster Reactome:REACT_21281 TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Homo sapiens Reactome:REACT_31084 TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Canis familiaris Reactome:REACT_33907 TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Danio rerio Reactome:REACT_34168 TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Sus scrofa Reactome:REACT_34256 TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Bos taurus Reactome:REACT_87914 TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Xenopus tropicalis Reactome:REACT_95400 TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Mus musculus activation of NF-kappaB transcription factor GOC:dph GOC:tb The directed movement of substances into, out of, or within the nucleus. Reactome:REACT_9004 Wikipedia:Nuclear_transport nucleus transport biological_process GO:0051169 nuclear transport The directed movement of substances into, out of, or within the nucleus. GOC:ai Reactome:REACT_9004 Import of PIC to the Host Nucleus, Homo sapiens The directed movement of substances into the nucleus. Reactome:REACT_10010 Reactome:REACT_32050 Reactome:REACT_91459 Reactome:REACT_97007 import into nucleus nucleus import substance nuclear import biological_process GO:0051170 nuclear import The directed movement of substances into the nucleus. GOC:ai Reactome:REACT_10010 snRNP nuclear import and release, Homo sapiens Reactome:REACT_32050 snRNP nuclear import and release, Xenopus tropicalis Reactome:REACT_91459 snRNP nuclear import and release, Mus musculus Reactome:REACT_97007 snRNP nuclear import and release, Danio rerio Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. regulation of nitrogen metabolic process regulation of nitrogen metabolism biological_process GO:0051171 regulation of nitrogen compound metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb regulation of nitrogen metabolic process GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. down regulation of nitrogen metabolic process down-regulation of nitrogen metabolic process downregulation of nitrogen metabolic process negative regulation of nitrogen metabolic process negative regulation of nitrogen metabolism inhibition of nitrogen metabolic process biological_process GO:0051172 negative regulation of nitrogen compound metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb negative regulation of nitrogen metabolic process GOC:tb Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. positive regulation of nitrogen metabolic process positive regulation of nitrogen metabolism up regulation of nitrogen metabolic process up-regulation of nitrogen metabolic process upregulation of nitrogen metabolic process activation of nitrogen metabolic process stimulation of nitrogen metabolic process biological_process GO:0051173 positive regulation of nitrogen compound metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb positive regulation of nitrogen metabolic process GOC:tb Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to or maintained in a specific location. establishment and maintenance of localization establishment and maintenance of position localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location biological_process GO:0051179 localization Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to or maintained in a specific location. GOC:ai localisation GOC:mah The selective interaction of a protein with specific molecules in the cytoplasm, thereby inhibiting its transport into other areas of the cell. cytoplasmic retention of protein cytoplasmic sequestration of protein cytoplasmic storage of protein maintenance of protein location in cytoplasm retention of protein in cytoplasm sequestering of protein in cytoplasm sequestration of protein in cytoplasm storage of protein in cytoplasm biological_process GO:0051220 cytoplasmic sequestering of protein The selective interaction of a protein with specific molecules in the cytoplasm, thereby inhibiting its transport into other areas of the cell. GOC:ai maintenance of protein location in cytoplasm GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of protein transport up-regulation of protein transport upregulation of protein transport activation of protein transport stimulation of protein transport biological_process GO:0051222 positive regulation of protein transport Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051223 regulation of protein transport Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of protein transport down-regulation of protein transport downregulation of protein transport inhibition of protein transport biological_process GO:0051224 negative regulation of protein transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location. establishment of localisation biological_process GO:0051234 establishment of localization The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location. GOC:ai establishment of localisation GOC:mah Any process in which a cell, substance or cellular entity, such as a protein complex or organelle, is maintained in a location and prevented from moving elsewhere. retention sequestering storage biological_process GO:0051235 maintenance of location Any process in which a cell, substance or cellular entity, such as a protein complex or organelle, is maintained in a location and prevented from moving elsewhere. GOC:ai GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA. regulation of RNA metabolism biological_process GO:0051252 regulation of RNA metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA. down regulation of RNA metabolic process down-regulation of RNA metabolic process downregulation of RNA metabolic process negative regulation of RNA metabolism inhibition of RNA metabolic process biological_process GO:0051253 negative regulation of RNA metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA. positive regulation of RNA metabolism up regulation of RNA metabolic process up-regulation of RNA metabolic process upregulation of RNA metabolic process activation of RNA metabolic process stimulation of RNA metabolic process biological_process GO:0051254 positive regulation of RNA metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA. GOC:ai A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. GO:0007001 GO:0051277 chromosome organisation biological_process chromosome organization and biogenesis maintenance of genome integrity nuclear genome maintenance GO:0051276 chromosome organization A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. GOC:ai GOC:dph GOC:jl GOC:mah chromosome organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized. centrosome organisation biological_process centrosome organization and biogenesis GO:0051297 centrosome organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized. GOC:ai GOC:dph GOC:jl GOC:mah centrosome organisation GOC:curators centrosome organization and biogenesis GOC:mah The replication of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized. centrosome replication biological_process GO:0051298 centrosome duplication The replication of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized. GOC:ai The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. Wikipedia:Cell_division biological_process GO:0051301 Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. cell division The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. GOC:di GOC:go_curators GOC:pr The directed movement of a chromosome to a specific location. chromosome positioning establishment of chromosome localisation biological_process GO:0051303 establishment of chromosome localization The directed movement of a chromosome to a specific location. GOC:ai establishment of chromosome localisation GOC:mah The alignment of chromosomes at the metaphase plate, a plane halfway between the poles of the spindle. chromosome congression biological_process GO:0051310 metaphase plate congression The alignment of chromosomes at the metaphase plate, a plane halfway between the poles of the spindle. GOC:ai chromosome congression GOC:ascb_2009 GOC:dph GOC:tb The alteration of chromosome structure from the condensed form to a relaxed disperse form. biological_process GO:0051312 chromosome decondensation The alteration of chromosome structure from the condensed form to a relaxed disperse form. GOC:ai The cell cycle 'gap' phase which is the interval between the completion of DNA segregation (usually by mitosis or meiosis) and the beginning of DNA synthesis. Wikipedia:G1_phase biological_process GO:0051318 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). G1 phase The cell cycle 'gap' phase which is the interval between the completion of DNA segregation (usually by mitosis or meiosis) and the beginning of DNA synthesis. GOC:mtg_cell_cycle The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation (usually by mitosis or meiosis). Wikipedia:G2_phase biological_process GO:0051319 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). G2 phase The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation (usually by mitosis or meiosis). GOC:mtg_cell_cycle The cell cycle phase, following G1, during which DNA synthesis takes place. Wikipedia:S_phase S-phase biological_process GO:0051320 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). S phase The cell cycle phase, following G1, during which DNA synthesis takes place. GOC:mtg_cell_cycle The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle. Wikipedia:Anaphase biological_process GO:0051322 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). anaphase The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle. GOC:mtg_cell_cycle The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell. Wikipedia:Metaphase biological_process GO:0051323 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). metaphase The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell. GOC:mtg_cell_cycle The cell cycle phase which is the first stage of M phase of meiosis and mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. Wikipedia:Prophase biological_process GO:0051324 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). prophase The cell cycle phase which is the first stage of M phase of meiosis and mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. GOC:mtg_cell_cycle The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs. resting phase Wikipedia:Interphase karyostasis biological_process GO:0051325 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). interphase The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs. GOC:mtg_cell_cycle The cell cycle phase which follows anaphase during M phase of mitosis and meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. Wikipedia:Telophase biological_process GO:0051326 note that this term should not be used for direct annotation. if you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic s-phase). to capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). telophase The cell cycle phase which follows anaphase during M phase of mitosis and meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. GOC:mtg_cell_cycle The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs. interphase of mitotic cell cycle biological_process GO:0051329 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic interphase The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs. GOC:mtg_cell_cycle Any process in which an organelle is transported to, and/or maintained in, a specific location. establishment and maintenance of organelle localization organelle localisation biological_process GO:0051640 organelle localization Any process in which an organelle is transported to, and/or maintained in, a specific location. GOC:ai organelle localisation GOC:mah A localization process that takes place at the cellular level; as a result of a cellular localization process, a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within or in the membrane of a cell. cellular localisation establishment and maintenance of cellular localization establishment and maintenance of localization in cell or cell membrane intracellular localization localization within cell biological_process GO:0051641 cellular localization A localization process that takes place at the cellular level; as a result of a cellular localization process, a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within or in the membrane of a cell. GOC:ai GOC:mah cellular localisation GOC:mah The directed movement of a substance or cellular entity, such as a protein complex or organelle, to a specific location within, or in the membrane of, a cell. establishment of localisation in cell establishment of intracellular localization establishment of localization within cell positioning within cell biological_process establishment of cellular localization GO:0051649 establishment of localization in cell The directed movement of a substance or cellular entity, such as a protein complex or organelle, to a specific location within, or in the membrane of, a cell. GOC:ai GOC:dph GOC:tb establishment of localisation in cell GOC:mah establishment of cellular localization GOC:dph GOC:tb Any process in which a substance or cellular entity, such as a protein complex or organelle, is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere. cellular retention cellular sequestering cellular storage intracellular retention intracellular sequestering intracellular storage maintenance of intracellular localization maintenance of localization within cell retention within cell sequestering within cell storage within cell biological_process maintenance of cellular localization maintenance of localization in cell GO:0051651 maintenance of location in cell Any process in which a substance or cellular entity, such as a protein complex or organelle, is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere. GOC:ai maintenance of cellular localization GOC:dph GOC:tb maintenance of localization in cell GOC:dph GOC:tb The directed movement of an organelle to a specific location. establishment of organelle localisation biological_process GO:0051656 establishment of organelle localization The directed movement of an organelle to a specific location. GOC:ai establishment of organelle localisation GOC:mah Any process in which a cell is transported to, and/or maintained in, a specific location. cell localization establishment and maintenance of cell localization establishment and maintenance of localization of cell localisation of cell biological_process GO:0051674 localization of cell Any process in which a cell is transported to, and/or maintained in, a specific location. GOC:ai localisation of cell GOC:mah Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. biological_process GO:0051716 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. GOC:bf GOC:jl Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0060255 regulation of macromolecule metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell. regulation of cellular localisation biological_process GO:0060341 regulation of cellular localization Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell. GOC:dph GOC:tb regulation of cellular localisation GOC:mah The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape. dph 2009-04-28T08:42:53Z differential growth biological_process GO:0060560 developmental growth involved in morphogenesis The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape. GOC:dph differential growth GOC:dph A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. dph 2010-02-08T02:43:11Z GO:0016044 Reactome:REACT_101524 Reactome:REACT_103082 Reactome:REACT_11123 Reactome:REACT_29278 Reactome:REACT_32337 Reactome:REACT_33741 Reactome:REACT_34084 Reactome:REACT_78213 Reactome:REACT_78288 Reactome:REACT_83546 Reactome:REACT_86557 Reactome:REACT_87431 Reactome:REACT_88307 Reactome:REACT_91154 Reactome:REACT_93714 Reactome:REACT_95586 Reactome:REACT_96516 Reactome:REACT_97881 cellular membrane organisation cellular membrane organization membrane organisation biological_process membrane organization and biogenesis GO:0061024 membrane organization A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. GOC:dph GOC:tb Reactome:REACT_101524 Membrane Trafficking, Dictyostelium discoideum Reactome:REACT_103082 Membrane Trafficking, Schizosaccharomyces pombe Reactome:REACT_11123 Membrane Trafficking, Homo sapiens Reactome:REACT_29278 Membrane Trafficking, Sus scrofa Reactome:REACT_32337 Membrane Trafficking, Taeniopygia guttata Reactome:REACT_33741 Membrane Trafficking, Bos taurus Reactome:REACT_34084 Membrane Trafficking, Caenorhabditis elegans Reactome:REACT_78213 Membrane Trafficking, Plasmodium falciparum Reactome:REACT_78288 Membrane Trafficking, Xenopus tropicalis Reactome:REACT_83546 Membrane Trafficking, Oryza sativa Reactome:REACT_86557 Membrane Trafficking, Arabidopsis thaliana Reactome:REACT_87431 Membrane Trafficking, Drosophila melanogaster Reactome:REACT_88307 Membrane Trafficking, Mus musculus Reactome:REACT_91154 Membrane Trafficking, Saccharomyces cerevisiae Reactome:REACT_93714 Membrane Trafficking, Danio rerio Reactome:REACT_95586 Membrane Trafficking, Gallus gallus Reactome:REACT_96516 Membrane Trafficking, Canis familiaris Reactome:REACT_97881 Membrane Trafficking, Rattus norvegicus cellular membrane organisation GOC:curators membrane organisation GOC:mah membrane organization and biogenesis GOC:mah The membrane organization process that joins two lipid bilayers to form a single membrane. dph 2010-02-08T02:48:06Z GO:0006944 Wikipedia:Lipid_bilayer_fusion cellular membrane fusion biological_process GO:0061025 membrane fusion The membrane organization process that joins two lipid bilayers to form a single membrane. GOC:dph GOC:tb The endoplasmic reticulum organization process that results in the structure of the endoplasmic reticulum being oriented in the cell. dph 2010-06-25T09:51:48Z biological_process GO:0061163 endoplasmic reticulum polarization The endoplasmic reticulum organization process that results in the structure of the endoplasmic reticulum being oriented in the cell. GOC:dph GOC:vw Any process that modulates a measurable attribute of any biological process, quality or function. regulation biological_process GO:0065007 biological regulation Any process that modulates a measurable attribute of any biological process, quality or function. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. regulation of biological attribute regulation of biological characteristic biological_process GO:0065008 regulation of biological quality Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. regulation of a molecular function biological_process GO:0065009 regulation of molecular function Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GOC:isa_complete An organelle lumen that is part of an intracellular organelle. cellular_component GO:0070013 intracellular organelle lumen An organelle lumen that is part of an intracellular organelle. GOC:mah A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix. anchoring cell junction cellular_component GO:0070161 anchoring junction A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix. ISBN:0815332181 anchoring cell junction GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. regulation of establishment of protein localisation biological_process GO:0070201 regulation of establishment of protein localization Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. GOC:BHF GOC:mah regulation of establishment of protein localisation GOC:mah The actin filament-based process in which cytoplasmic actin filaments slide past one another resulting in contraction of all or part of the cell body. biological_process GO:0070252 actin-mediated cell contraction The actin filament-based process in which cytoplasmic actin filaments slide past one another resulting in contraction of all or part of the cell body. GOC:mah A process in which a protein is transported to, or maintained in, a location within the mitochondrion. midori 2009-04-24T02:31:18Z protein localisation in mitochondrion protein localization in mitochondrion biological_process GO:0070585 protein localization to mitochondrion A process in which a protein is transported to, or maintained in, a location within the mitochondrion. GOC:ecd protein localisation in mitochondrion GOC:mah protein localization in mitochondrion GOC:curators Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. midori 2009-06-16T04:08:29Z cellular macromolecule localisation biological_process GO:0070727 cellular macromolecule localization Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GOC:mah cellular macromolecule localisation GOC:mah Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. midori 2009-08-27T04:41:45Z biological_process GO:0070887 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to chemical stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. GOC:mah The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. midori 2009-09-15T03:00:51Z biological_process GO:0070925 organelle assembly The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:mah A process in which a protein is transported to, or maintained in, a location within the endoplasmic reticulum. midori 2009-10-02T12:43:34Z protein localisation in endoplasmic reticulum protein localization in ER protein localization in endoplasmic reticulum biological_process GO:0070972 protein localization to endoplasmic reticulum A process in which a protein is transported to, or maintained in, a location within the endoplasmic reticulum. GOC:mah protein localisation in endoplasmic reticulum GOC:mah protein localization in ER GOC:mah protein localization in endoplasmic reticulum GOC:curators A cellular process that results in a change in the spatial configuration of a DNA molecule. A conformation change can bend DNA, or alter the, twist, writhe, or linking number of a DNA molecule. midori 2009-11-09T11:36:34Z DNA conformation modification biological_process GO:0071103 DNA conformation change A cellular process that results in a change in the spatial configuration of a DNA molecule. A conformation change can bend DNA, or alter the, twist, writhe, or linking number of a DNA molecule. GOC:mah DNA conformation modification GOC:mah A process in which a protein is transported to, or maintained at, the centrosome. midori 2010-01-12T02:09:45Z protein localisation to centrosome biological_process GO:0071539 protein localization to centrosome A process in which a protein is transported to, or maintained at, the centrosome. GOC:ecd protein localisation to centrosome GOC:mah The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. midori 2010-03-08T02:15:14Z biological_process GO:0071702 organic substance transport The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. CHEBI:50860 GOC:mah The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. midori 2010-03-08T03:32:18Z organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism biological_process GO:0071704 organic substance metabolic process The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. CHEBI:50860 GOC:mah The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. midori 2010-03-08T03:56:28Z biological_process GO:0071705 nitrogen compound transport The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. CHEBI:51143 GOC:mah A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. midori 2010-09-10T01:39:16Z GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level biological_process GO:0071840 cellular component organization or biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:mah cellular component organisation or biogenesis GOC:mah cellular component organisation or biogenesis at cellular level GOC:mah The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. midori 2010-09-15T02:14:33Z DNA anabolism DNA biosynthesis DNA formation DNA synthesis biological_process GO:0071897 DNA biosynthetic process The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. GOC:mah DNA anabolism GOC:mah DNA biosynthesis GOC:mah DNA formation GOC:mah DNA synthesis GOC:mah The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures. midori 2010-10-04T01:51:47Z cellular_component GO:0071944 cell periphery The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures. GOC:mah The directed movement of a protein to a specific location on or in an organelle. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle. midori 2011-02-14T01:56:51Z establishment of protein localisation to organelle biological_process GO:0072594 establishment of protein localization to organelle The directed movement of a protein to a specific location on or in an organelle. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle. GOC:mah establishment of protein localisation to organelle GOC:mah A process in which a protein is transported to, or maintained in, a specific location in a membrane. midori 2011-02-14T02:35:18Z protein localisation in membrane protein localization in membrane biological_process GO:0072657 protein localization to membrane A process in which a protein is transported to, or maintained in, a specific location in a membrane. GOC:mah protein localisation in membrane GOC:mah protein localization in membrane GOC:curators A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane. midori 2011-02-14T02:43:05Z protein localisation in plasma membrane protein localization in plasma membrane biological_process GO:0072659 protein localization to plasma membrane A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane. GOC:mah protein localisation in plasma membrane GOC:mah protein localization in plasma membrane GOC:curators A process in which a protein is transported to, or maintained at, a location in a peroxisome. midori 2011-02-14T02:50:04Z protein localisation to peroxisome biological_process GO:0072662 protein localization to peroxisome A process in which a protein is transported to, or maintained at, a location in a peroxisome. GOC:ecd protein localisation to peroxisome GOC:mah A process in which a protein is transported to, or maintained at, a location in a vacuole. midori 2011-02-14T02:55:35Z protein localisation to vacuole biological_process GO:0072665 protein localization to vacuole A process in which a protein is transported to, or maintained at, a location in a vacuole. GOC:ecd protein localisation to vacuole GOC:mah A cellular protein localization process in which a protein is transported to, or maintained at, a location within the microtubule cytoskeleton. midori 2012-04-11T01:19:35Z protein localisation to microtubule cytoskeleton biological_process GO:0072698 protein localization to microtubule cytoskeleton A cellular protein localization process in which a protein is transported to, or maintained at, a location within the microtubule cytoskeleton. GOC:mah protein localisation to microtubule cytoskeleton GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. donghui 2009-04-22T04:30:52Z biological_process GO:0080090 regulation of primary metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. PMID:19211694 Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. tanyaberardini 2009-10-23T11:21:38Z biological_process GO:0090087 regulation of peptide transport Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph GOC:tb A process that is carried out at the cellular level which results in the separation of a single continuous membrane into two membranes. tanyaberardini 2009-12-08T03:06:36Z biological_process GO:0090148 membrane fission A process that is carried out at the cellular level which results in the separation of a single continuous membrane into two membranes. GOC:ascb_2009 GOC:dph GOC:tb A process in which a protein is transported to, or maintained in, a nuclear pore. tanyaberardini 2009-12-18T12:05:01Z protein localisation to nuclear pore biological_process GO:0090204 protein localization to nuclear pore A process in which a protein is transported to, or maintained in, a nuclear pore. GOC:dph GOC:rb GOC:tb protein localisation to nuclear pore GOC:mah Any cellular metabolic process involving nucleic acids. tanyaberardini 2010-04-07T10:18:47Z biological_process GO:0090304 nucleic acid metabolic process Any cellular metabolic process involving nucleic acids. GOC:dph GOC:tb The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis. tanyaberardini 2010-04-07T10:26:30Z nucleic acid cleavage biological_process GO:0090305 nucleic acid phosphodiester bond hydrolysis The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis. GOC:dph GOC:tb nucleic acid cleavage GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells. tanyaberardini 2010-04-16T03:45:07Z biological_process GO:0090316 positive regulation of intracellular protein transport Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells. GOC:tb Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells. tanyaberardini 2010-04-16T03:45:07Z biological_process GO:0090317 negative regulation of intracellular protein transport Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells. GOC:tb A process in which a protein is transported to, or maintained at, a location within a nuclear envelope. tanyaberardini 2012-07-30T01:50:41Z protein localization in nuclear envelope biological_process GO:0090435 protein localization to nuclear envelope A process in which a protein is transported to, or maintained at, a location within a nuclear envelope. GOC:tb protein localization in nuclear envelope GOC:curators Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure. paola 2011-09-23T02:31:01Z molecular_function GO:0097159 organic cyclic compound binding Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure. CHEBI:33832 GOC:sjw PMID:7583672 A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. paola 2011-11-23T09:45:24Z execution phase of apoptotic process apoptosis biological_process GO:0097194 execution phase of apoptosis A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GOC:mtg_apoptosis PMID:21760595 A process in which a protein is transported to, or maintained at, a location within a cellular bud neck. paola 2012-03-20T03:39:20Z protein localisation to bud neck protein localization to cellular bud neck biological_process GO:0097271 protein localization to bud neck A process in which a protein is transported to, or maintained at, a location within a cellular bud neck. GOC:rb PMID:22344253 protein localisation to bud neck GOC:mah An arrangement of closely apposed microtubules running parallel to each other. paola 2012-11-07T15:01:27Z NIF_Subcellular:sao1872343973 microtubule fascicle cellular_component GO:0097427 microtubule bundle An arrangement of closely apposed microtubules running parallel to each other. NIF_Subcellular:sao1872343973 Any constituent part of a neuron, the basic cellular unit of nervous tissue. A typical neuron consists of a cell body (often called the soma), an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. paola 2012-12-19T16:53:50Z cellular_component GO:0097458 neuron part Any constituent part of a neuron, the basic cellular unit of nervous tissue. A typical neuron consists of a cell body (often called the soma), an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. GOC:pr http://en.wikipedia.org/wiki/Neuron The cellular synthesis of RNA on a template of nucleic acid (DNA or RNA). paola 2014-10-01T13:49:27Z biological_process GO:0097659 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. nucleic acid-templated transcription The cellular synthesis of RNA on a template of nucleic acid (DNA or RNA). GOC:pr GOC:txnOH GOC:vw A cellular process that results in the assembly of one or more centrioles. davidos 2013-10-22T15:55:22Z biological_process GO:0098534 centriole assembly A cellular process that results in the assembly of one or more centrioles. GOC:dos PMID:24075808 The attachment, via cell adhesion molecules, of a cell to either another cell of the same organism, or to an underlying substrate of the same organism such as the extracellular matrix. davidos 2014-04-15T15:59:10Z biological_process GO:0098602 single organism cell adhesion The attachment, via cell adhesion molecules, of a cell to either another cell of the same organism, or to an underlying substrate of the same organism such as the extracellular matrix. GOC:dos Any subdivision of a chromosome along its length. chromosome region cellular_component GO:0098687 Chromosomal regions include parts that are not part of the chromatin. Examples include the kinetochore. chromosomal region Any subdivision of a chromosome along its length. GOC:dos One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. biological_process GO:0098763 mitotic cell cycle phase One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. GOC:dos The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. biological_process GO:0098813 nuclear chromosome segregation The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. GOC:dos Any process that modulates the frequency, rate or extent of protein localization to nucleus. bf 2012-03-12T01:23:44Z regulation of protein localisation to nucleus regulation of protein localization in cell nucleus regulation of protein localization in nucleus biological_process GO:1900180 regulation of protein localization to nucleus Any process that modulates the frequency, rate or extent of protein localization to nucleus. GOC:TermGenie regulation of protein localisation to nucleus GOC:TermGenie regulation of protein localization in cell nucleus GOC:TermGenie regulation of protein localization in nucleus GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleus. bf 2012-03-12T01:23:48Z down regulation of protein localisation to nucleus down regulation of protein localization in cell nucleus down regulation of protein localization in nucleus down regulation of protein localization to nucleus down-regulation of protein localisation to nucleus down-regulation of protein localization in cell nucleus down-regulation of protein localization in nucleus down-regulation of protein localization to nucleus downregulation of protein localisation to nucleus downregulation of protein localization in cell nucleus downregulation of protein localization in nucleus downregulation of protein localization to nucleus negative regulation of protein localisation to nucleus negative regulation of protein localization in cell nucleus negative regulation of protein localization in nucleus inhibition of protein localisation to nucleus inhibition of protein localization in cell nucleus inhibition of protein localization in nucleus inhibition of protein localization to nucleus biological_process GO:1900181 negative regulation of protein localization to nucleus Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleus. GOC:TermGenie down regulation of protein localisation to nucleus GOC:TermGenie down regulation of protein localization in cell nucleus GOC:TermGenie down regulation of protein localization in nucleus GOC:TermGenie down regulation of protein localization to nucleus GOC:TermGenie down-regulation of protein localisation to nucleus GOC:TermGenie down-regulation of protein localization in cell nucleus GOC:TermGenie down-regulation of protein localization in nucleus GOC:TermGenie down-regulation of protein localization to nucleus GOC:TermGenie downregulation of protein localisation to nucleus GOC:TermGenie downregulation of protein localization in cell nucleus GOC:TermGenie downregulation of protein localization in nucleus GOC:TermGenie downregulation of protein localization to nucleus GOC:TermGenie negative regulation of protein localisation to nucleus GOC:TermGenie negative regulation of protein localization in cell nucleus GOC:TermGenie negative regulation of protein localization in nucleus GOC:TermGenie inhibition of protein localisation to nucleus GOC:TermGenie inhibition of protein localization in cell nucleus GOC:TermGenie inhibition of protein localization in nucleus GOC:TermGenie inhibition of protein localization to nucleus GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to nucleus. bf 2012-03-12T01:23:52Z activation of protein localization in nucleus positive regulation of protein localisation to nucleus positive regulation of protein localization in cell nucleus positive regulation of protein localization in nucleus up regulation of protein localisation to nucleus up regulation of protein localization in cell nucleus up regulation of protein localization in nucleus up regulation of protein localization to nucleus up-regulation of protein localisation to nucleus up-regulation of protein localization in cell nucleus up-regulation of protein localization in nucleus up-regulation of protein localization to nucleus upregulation of protein localisation to nucleus upregulation of protein localization in cell nucleus upregulation of protein localization in nucleus upregulation of protein localization to nucleus activation of protein localisation to nucleus activation of protein localization in cell nucleus activation of protein localization to nucleus biological_process GO:1900182 positive regulation of protein localization to nucleus Any process that activates or increases the frequency, rate or extent of protein localization to nucleus. GOC:TermGenie activation of protein localization in nucleus GOC:TermGenie positive regulation of protein localisation to nucleus GOC:TermGenie positive regulation of protein localization in cell nucleus GOC:TermGenie positive regulation of protein localization in nucleus GOC:TermGenie up regulation of protein localisation to nucleus GOC:TermGenie up regulation of protein localization in cell nucleus GOC:TermGenie up regulation of protein localization in nucleus GOC:TermGenie up regulation of protein localization to nucleus GOC:TermGenie up-regulation of protein localisation to nucleus GOC:TermGenie up-regulation of protein localization in cell nucleus GOC:TermGenie up-regulation of protein localization in nucleus GOC:TermGenie up-regulation of protein localization to nucleus GOC:TermGenie upregulation of protein localisation to nucleus GOC:TermGenie upregulation of protein localization in cell nucleus GOC:TermGenie upregulation of protein localization in nucleus GOC:TermGenie upregulation of protein localization to nucleus GOC:TermGenie activation of protein localisation to nucleus GOC:TermGenie activation of protein localization in cell nucleus GOC:TermGenie activation of protein localization to nucleus GOC:TermGenie The chemical reactions and pathways involving organic cyclic compound. bf 2012-09-14T09:03:51Z organic cyclic compound metabolism biological_process GO:1901360 organic cyclic compound metabolic process The chemical reactions and pathways involving organic cyclic compound. GOC:TermGenie organic cyclic compound metabolism GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. bf 2012-09-14T09:05:04Z organic cyclic compound breakdown organic cyclic compound catabolism organic cyclic compound degradation biological_process GO:1901361 organic cyclic compound catabolic process The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. GOC:TermGenie organic cyclic compound breakdown GOC:TermGenie organic cyclic compound catabolism GOC:TermGenie organic cyclic compound degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of organic cyclic compound. bf 2012-09-14T09:05:22Z organic cyclic compound anabolism organic cyclic compound biosynthesis organic cyclic compound formation organic cyclic compound synthesis biological_process GO:1901362 organic cyclic compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic cyclic compound. GOC:TermGenie organic cyclic compound anabolism GOC:TermGenie organic cyclic compound biosynthesis GOC:TermGenie organic cyclic compound formation GOC:TermGenie organic cyclic compound synthesis GOC:TermGenie Interacting selectively and non-covalently with heterocyclic compound. bf 2012-09-14T13:53:50Z molecular_function GO:1901363 heterocyclic compound binding Interacting selectively and non-covalently with heterocyclic compound. GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon. pr 2012-11-05T11:04:36Z organic molecular entity breakdown organic molecular entity catabolic process organic molecular entity catabolism organic molecular entity degradation organic substance breakdown organic substance catabolism organic substance degradation biological_process GO:1901575 organic substance catabolic process The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon. GOC:TermGenie GOC:pr organic molecular entity breakdown GOC:TermGenie organic molecular entity catabolism GOC:TermGenie organic molecular entity degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. pr 2012-11-05T11:04:40Z organic molecular entity anabolism organic molecular entity biosynthesis organic molecular entity biosynthetic process organic molecular entity formation organic molecular entity synthesis organic substance anabolism organic substance biosynthesis organic substance formation organic substance synthesis biological_process GO:1901576 organic substance biosynthetic process The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. GOC:TermGenie GOC:pr organic molecular entity anabolism GOC:TermGenie organic molecular entity biosynthesis GOC:TermGenie organic molecular entity formation GOC:TermGenie organic molecular entity synthesis GOC:TermGenie Any process that modulates the frequency, rate or extent of intracellular signal transduction. bf 2013-12-02T11:32:52Z GO:0010627 regulation of intracellular signaling cascade regulation of intracellular signaling chain regulation of intracellular protein kinase cascade regulation of intracellular signal transduction pathway regulation of signal transmission via intracellular cascade biological_process regulation of intracellular signaling pathway regulation of signal transduction via intracellular signaling cascade GO:1902531 regulation of intracellular signal transduction Any process that modulates the frequency, rate or extent of intracellular signal transduction. GOC:TermGenie GOC:dph GOC:signaling GOC:tb regulation of intracellular signaling cascade GOC:TermGenie regulation of intracellular signaling chain GOC:TermGenie regulation of intracellular signal transduction pathway GOC:TermGenie regulation of signal transmission via intracellular cascade GOC:TermGenie regulation of intracellular signaling pathway GOC:TermGenie regulation of signal transduction via intracellular signaling cascade GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction. bf 2013-12-02T11:33:01Z GO:0010741 down regulation of intracellular signal transduction down regulation of intracellular signaling chain down-regulation of intracellular signal transduction down-regulation of intracellular signaling chain downregulation of intracellular signal transduction downregulation of intracellular signaling chain negative regulation of intracellular protein kinase cascade negative regulation of intracellular signaling cascade negative regulation of intracellular signaling chain down regulation of intracellular signal transduction pathway down regulation of intracellular signaling cascade down regulation of signal transmission via intracellular cascade down-regulation of intracellular signal transduction pathway downregulation of intracellular signal transduction pathway downregulation of intracellular signaling cascade downregulation of signal transmission via intracellular cascade inhibition of intracellular signal transduction inhibition of intracellular signal transduction pathway inhibition of intracellular signaling cascade inhibition of intracellular signaling chain inhibition of signal transmission via intracellular cascade negative regulation of intracellular signal transduction pathway negative regulation of signal transmission via intracellular cascade biological_process down regulation of intracellular signaling pathway down regulation of signal transduction via intracellular signaling cascade down-regulation of intracellular signaling cascade down-regulation of intracellular signaling pathway down-regulation of signal transduction via intracellular signaling cascade down-regulation of signal transmission via intracellular cascade downregulation of intracellular signaling pathway downregulation of signal transduction via intracellular signaling cascade inhibition of intracellular signaling pathway inhibition of signal transduction via intracellular signaling cascade negative regulation of intracellular signaling pathway negative regulation of signal transduction via intracellular signaling cascade GO:1902532 negative regulation of intracellular signal transduction Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction. GOC:TermGenie GOC:dph GOC:signaling GOC:tb down regulation of intracellular signal transduction GOC:TermGenie down regulation of intracellular signaling chain GOC:TermGenie down-regulation of intracellular signal transduction GOC:TermGenie down-regulation of intracellular signaling chain GOC:TermGenie downregulation of intracellular signal transduction GOC:TermGenie downregulation of intracellular signaling chain GOC:TermGenie negative regulation of intracellular signaling cascade GOC:TermGenie negative regulation of intracellular signaling chain GOC:TermGenie down regulation of intracellular signal transduction pathway GOC:TermGenie down regulation of intracellular signaling cascade GOC:TermGenie down regulation of signal transmission via intracellular cascade GOC:TermGenie down-regulation of intracellular signal transduction pathway GOC:TermGenie downregulation of intracellular signal transduction pathway GOC:TermGenie downregulation of intracellular signaling cascade GOC:TermGenie downregulation of signal transmission via intracellular cascade GOC:TermGenie inhibition of intracellular signal transduction GOC:TermGenie inhibition of intracellular signal transduction pathway GOC:TermGenie inhibition of intracellular signaling cascade GOC:TermGenie inhibition of intracellular signaling chain GOC:TermGenie inhibition of signal transmission via intracellular cascade GOC:TermGenie negative regulation of intracellular signal transduction pathway GOC:TermGenie negative regulation of signal transmission via intracellular cascade GOC:TermGenie down regulation of intracellular signaling pathway GOC:TermGenie down regulation of signal transduction via intracellular signaling cascade GOC:TermGenie down-regulation of intracellular signaling cascade GOC:TermGenie down-regulation of intracellular signaling pathway GOC:TermGenie down-regulation of signal transduction via intracellular signaling cascade GOC:TermGenie down-regulation of signal transmission via intracellular cascade GOC:TermGenie downregulation of intracellular signaling pathway GOC:TermGenie downregulation of signal transduction via intracellular signaling cascade GOC:TermGenie inhibition of intracellular signaling pathway GOC:TermGenie inhibition of signal transduction via intracellular signaling cascade GOC:TermGenie negative regulation of intracellular signaling pathway GOC:TermGenie negative regulation of signal transduction via intracellular signaling cascade GOC:TermGenie Any process that activates or increases the frequency, rate or extent of intracellular signal transduction. bf 2013-12-02T11:33:10Z GO:0010740 positive regulation of intracellular signaling chain up regulation of intracellular signal transduction up regulation of intracellular signaling chain up-regulation of intracellular signal transduction up-regulation of intracellular signaling chain upregulation of intracellular signal transduction upregulation of intracellular signaling chain activation of intracellular signal transduction activation of intracellular signal transduction pathway activation of intracellular signaling cascade activation of intracellular signaling chain activation of signal transmission via intracellular cascade positive regulation of intracellular protein kinase cascade positive regulation of intracellular signal transduction pathway positive regulation of signal transmission via intracellular cascade up regulation of intracellular signal transduction pathway up regulation of signal transmission via intracellular cascade up-regulation of intracellular signal transduction pathway up-regulation of signal transmission via intracellular cascade upregulation of intracellular signal transduction pathway upregulation of signal transmission via intracellular cascade biological_process activation of intracellular signaling pathway activation of signal transduction via intracellular signaling cascade positive regulation of intracellular signaling cascade positive regulation of intracellular signaling pathway positive regulation of signal transduction via intracellular signaling cascade up regulation of intracellular signaling cascade up regulation of intracellular signaling pathway up regulation of signal transduction via intracellular signaling cascade up-regulation of intracellular signaling cascade up-regulation of intracellular signaling pathway up-regulation of signal transduction via intracellular signaling cascade upregulation of intracellular signaling cascade upregulation of intracellular signaling pathway upregulation of signal transduction via intracellular signaling cascade GO:1902533 positive regulation of intracellular signal transduction Any process that activates or increases the frequency, rate or extent of intracellular signal transduction. GOC:BHF GOC:TermGenie GOC:dph GOC:signaling GOC:tb positive regulation of intracellular signaling chain GOC:TermGenie up regulation of intracellular signal transduction GOC:TermGenie up regulation of intracellular signaling chain GOC:TermGenie up-regulation of intracellular signal transduction GOC:TermGenie up-regulation of intracellular signaling chain GOC:TermGenie upregulation of intracellular signal transduction GOC:TermGenie upregulation of intracellular signaling chain GOC:TermGenie activation of intracellular signal transduction GOC:TermGenie activation of intracellular signal transduction pathway GOC:TermGenie activation of intracellular signaling cascade GOC:TermGenie activation of intracellular signaling chain GOC:TermGenie activation of signal transmission via intracellular cascade GOC:TermGenie positive regulation of intracellular signal transduction pathway GOC:TermGenie positive regulation of signal transmission via intracellular cascade GOC:TermGenie up regulation of intracellular signal transduction pathway GOC:TermGenie up regulation of signal transmission via intracellular cascade GOC:TermGenie up-regulation of intracellular signal transduction pathway GOC:TermGenie up-regulation of signal transmission via intracellular cascade GOC:TermGenie upregulation of intracellular signal transduction pathway GOC:TermGenie upregulation of signal transmission via intracellular cascade GOC:TermGenie activation of intracellular signaling pathway GOC:TermGenie activation of signal transduction via intracellular signaling cascade GOC:TermGenie positive regulation of intracellular signaling cascade GOC:TermGenie positive regulation of intracellular signaling pathway GOC:TermGenie positive regulation of signal transduction via intracellular signaling cascade GOC:TermGenie up regulation of intracellular signaling cascade GOC:TermGenie up regulation of intracellular signaling pathway GOC:TermGenie up regulation of signal transduction via intracellular signaling cascade GOC:TermGenie up-regulation of intracellular signaling cascade GOC:TermGenie up-regulation of intracellular signaling pathway GOC:TermGenie up-regulation of signal transduction via intracellular signaling cascade GOC:TermGenie upregulation of intracellular signaling cascade GOC:TermGenie upregulation of intracellular signaling pathway GOC:TermGenie upregulation of signal transduction via intracellular signaling cascade GOC:TermGenie A process in which a protein is transported to, or maintained in, a location within a nucleolus. mah 2013-12-10T16:25:28Z protein localisation in nucleolus protein localisation to nucleolus protein localization in nucleolus biological_process GO:1902570 protein localization to nucleolus A process in which a protein is transported to, or maintained in, a location within a nucleolus. GOC:TermGenie PMID:22809626 protein localisation in nucleolus GOC:TermGenie protein localisation to nucleolus GOC:TermGenie protein localization in nucleolus GOC:TermGenie A localization which involves only one organism. jl 2013-12-18T13:51:04Z single organism localization biological_process GO:1902578 single-organism localization A localization which involves only one organism. GOC:jl GO_REF:0000089 PMID:1234 single organism localization GOC:TermGenie A cellular localization which involves only one organism. jl 2013-12-18T14:04:32Z single organism cellular localization biological_process GO:1902580 single-organism cellular localization A cellular localization which involves only one organism. GOC:TermGenie GOC:jl GO_REF:0000089 single organism cellular localization GOC:TermGenie An intracellular transport which involves only one organism. jl 2013-12-18T14:04:50Z single organism intracellular transport biological_process GO:1902582 single-organism intracellular transport An intracellular transport which involves only one organism. GOC:TermGenie GOC:jl GO_REF:0000089 single organism intracellular transport GOC:TermGenie An organelle organization which involves only one organism. jl 2013-12-19T15:25:51Z single organism organelle organization biological_process GO:1902589 single-organism organelle organization An organelle organization which involves only one organism. GOC:TermGenie GOC:jl GO_REF:0000089 single organism organelle organization GOC:TermGenie A nuclear import which involves only one organism. jl 2013-12-19T15:26:34Z single organism nuclear import biological_process GO:1902593 single-organism nuclear import A nuclear import which involves only one organism. GOC:TermGenie GOC:jl GO_REF:0000089 single organism nuclear import GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process. jl 2014-02-05T16:32:01Z down regulation of RNA anabolism down regulation of RNA biosynthesis down regulation of RNA biosynthetic process down regulation of RNA formation down regulation of RNA synthesis down-regulation of RNA anabolism down-regulation of RNA biosynthesis down-regulation of RNA biosynthetic process down-regulation of RNA formation down-regulation of RNA synthesis downregulation of RNA anabolism downregulation of RNA biosynthesis downregulation of RNA biosynthetic process downregulation of RNA formation downregulation of RNA synthesis negative regulation of RNA anabolism negative regulation of RNA biosynthesis negative regulation of RNA formation negative regulation of RNA synthesis inhibition of RNA anabolism inhibition of RNA biosynthesis inhibition of RNA biosynthetic process inhibition of RNA formation inhibition of RNA synthesis biological_process GO:1902679 negative regulation of RNA biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process. GO:jl GOC:TermGenie GO_REF:0000058 down regulation of RNA anabolism GOC:TermGenie down regulation of RNA biosynthesis GOC:TermGenie down regulation of RNA biosynthetic process GOC:TermGenie down regulation of RNA formation GOC:TermGenie down regulation of RNA synthesis GOC:TermGenie down-regulation of RNA anabolism GOC:TermGenie down-regulation of RNA biosynthesis GOC:TermGenie down-regulation of RNA biosynthetic process GOC:TermGenie down-regulation of RNA formation GOC:TermGenie down-regulation of RNA synthesis GOC:TermGenie downregulation of RNA anabolism GOC:TermGenie downregulation of RNA biosynthesis GOC:TermGenie downregulation of RNA biosynthetic process GOC:TermGenie downregulation of RNA formation GOC:TermGenie downregulation of RNA synthesis GOC:TermGenie negative regulation of RNA anabolism GOC:TermGenie negative regulation of RNA biosynthesis GOC:TermGenie negative regulation of RNA formation GOC:TermGenie negative regulation of RNA synthesis GOC:TermGenie inhibition of RNA anabolism GOC:TermGenie inhibition of RNA biosynthesis GOC:TermGenie inhibition of RNA biosynthetic process GOC:TermGenie inhibition of RNA formation GOC:TermGenie inhibition of RNA synthesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process. jl 2014-02-05T16:32:10Z positive regulation of RNA anabolism positive regulation of RNA biosynthesis positive regulation of RNA formation positive regulation of RNA synthesis up regulation of RNA anabolism up regulation of RNA biosynthesis up regulation of RNA biosynthetic process up regulation of RNA formation up regulation of RNA synthesis up-regulation of RNA anabolism up-regulation of RNA biosynthesis up-regulation of RNA biosynthetic process up-regulation of RNA formation up-regulation of RNA synthesis upregulation of RNA anabolism upregulation of RNA biosynthesis upregulation of RNA biosynthetic process upregulation of RNA formation upregulation of RNA synthesis activation of RNA anabolism activation of RNA biosynthesis activation of RNA biosynthetic process activation of RNA formation activation of RNA synthesis biological_process GO:1902680 positive regulation of RNA biosynthetic process Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process. GO:jl GOC:TermGenie GO_REF:0000058 positive regulation of RNA anabolism GOC:TermGenie positive regulation of RNA biosynthesis GOC:TermGenie positive regulation of RNA formation GOC:TermGenie positive regulation of RNA synthesis GOC:TermGenie up regulation of RNA anabolism GOC:TermGenie up regulation of RNA biosynthesis GOC:TermGenie up regulation of RNA biosynthetic process GOC:TermGenie up regulation of RNA formation GOC:TermGenie up regulation of RNA synthesis GOC:TermGenie up-regulation of RNA anabolism GOC:TermGenie up-regulation of RNA biosynthesis GOC:TermGenie up-regulation of RNA biosynthetic process GOC:TermGenie up-regulation of RNA formation GOC:TermGenie up-regulation of RNA synthesis GOC:TermGenie upregulation of RNA anabolism GOC:TermGenie upregulation of RNA biosynthesis GOC:TermGenie upregulation of RNA biosynthetic process GOC:TermGenie upregulation of RNA formation GOC:TermGenie upregulation of RNA synthesis GOC:TermGenie activation of RNA anabolism GOC:TermGenie activation of RNA biosynthesis GOC:TermGenie activation of RNA biosynthetic process GOC:TermGenie activation of RNA formation GOC:TermGenie activation of RNA synthesis GOC:TermGenie A process that is part of the mitotic cell cycle. jl 2014-05-22T14:22:34Z biological_process GO:1903047 mitotic cell cycle process A process that is part of the mitotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 A process in which a protein is transported to, or maintained in, the location of an actin cytoskeleton. mah 2014-06-16T11:27:09Z protein localisation in actin cytoskeleton protein localisation to actin cytoskeleton protein localization in actin cytoskeleton biological_process GO:1903119 protein localization to actin cytoskeleton A process in which a protein is transported to, or maintained in, the location of an actin cytoskeleton. GOC:TermGenie GO_REF:0000087 PMID:24798735 protein localisation in actin cytoskeleton GOC:TermGenie protein localisation to actin cytoskeleton GOC:TermGenie protein localization in actin cytoskeleton GOC:TermGenie A process in which a protein is transported to, or maintained in, the location of an actin filament bundle. mah 2014-06-16T11:27:16Z protein localisation in actin filament bundle protein localisation to actin filament bundle protein localization in actin filament bundle biological_process protein localization to actin cable GO:1903120 protein localization to actin filament bundle A process in which a protein is transported to, or maintained in, the location of an actin filament bundle. GOC:TermGenie GO_REF:0000087 PMID:24798735 protein localisation in actin filament bundle GOC:TermGenie protein localisation to actin filament bundle GOC:TermGenie protein localization in actin filament bundle GOC:TermGenie protein localization to actin cable GOC:mah A process in which a protein is transported to, or maintained in, a location within a nuclear body. mah 2014-09-01T13:57:11Z protein localisation in nuclear body protein localisation to nuclear body protein localization in nuclear body biological_process GO:1903405 protein localization to nuclear body A process in which a protein is transported to, or maintained in, a location within a nuclear body. GOC:TermGenie GO_REF:0000087 PMID:24713849 protein localisation in nuclear body GOC:TermGenie protein localisation to nuclear body GOC:TermGenie protein localization in nuclear body GOC:TermGenie Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription. pr 2014-10-01T14:44:47Z biological_process GO:1903506 regulation of nucleic acid-templated transcription Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription. GOC:TermGenie GOC:pr GOC:txnOH GOC:vw GO_REF:0000058 Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription. pr 2014-10-01T14:44:56Z down regulation of nucleic acid-templated transcription down-regulation of nucleic acid-templated transcription downregulation of nucleic acid-templated transcription inhibition of nucleic acid-templated transcription biological_process GO:1903507 negative regulation of nucleic acid-templated transcription Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription. GOC:TermGenie GOC:pr GOC:txnOH GOC:vw GO_REF:0000058 down regulation of nucleic acid-templated transcription GOC:TermGenie down-regulation of nucleic acid-templated transcription GOC:TermGenie downregulation of nucleic acid-templated transcription GOC:TermGenie inhibition of nucleic acid-templated transcription GOC:TermGenie Any process that activates or increases the frequency, rate or extent of nucleic acid-templated transcription. pr 2014-10-01T14:45:04Z up regulation of nucleic acid-templated transcription up-regulation of nucleic acid-templated transcription upregulation of nucleic acid-templated transcription activation of nucleic acid-templated transcription biological_process GO:1903508 positive regulation of nucleic acid-templated transcription Any process that activates or increases the frequency, rate or extent of nucleic acid-templated transcription. GOC:TermGenie GOC:pr GOC:txnOH GOC:vw GO_REF:0000058 up regulation of nucleic acid-templated transcription GOC:TermGenie up-regulation of nucleic acid-templated transcription GOC:TermGenie upregulation of nucleic acid-templated transcription GOC:TermGenie activation of nucleic acid-templated transcription GOC:TermGenie Any process that modulates the frequency, rate or extent of protein targeting. al 2014-10-08T14:49:03Z regulation of protein sorting along secretory pathway biological_process regulation of nascent polypeptide association GO:1903533 regulation of protein targeting Any process that modulates the frequency, rate or extent of protein targeting. GOC:TermGenie GO_REF:0000058 regulation of protein sorting along secretory pathway GOC:TermGenie regulation of nascent polypeptide association GOC:TermGenie Any process that modulates the frequency, rate or extent of cytoplasmic transport. jl 2014-11-24T13:38:17Z regulation of cytoplasmic streaming biological_process GO:1903649 regulation of cytoplasmic transport Any process that modulates the frequency, rate or extent of cytoplasmic transport. GOC:TermGenie GO_REF:0000058 PMID:25049409 regulation of cytoplasmic streaming GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic transport. jl 2014-11-24T13:38:26Z down regulation of cytoplasmic transport down-regulation of cytoplasmic transport downregulation of cytoplasmic transport down regulation of cytoplasmic streaming down-regulation of cytoplasmic streaming downregulation of cytoplasmic streaming inhibition of cytoplasmic streaming inhibition of cytoplasmic transport negative regulation of cytoplasmic streaming biological_process GO:1903650 negative regulation of cytoplasmic transport Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic transport. GOC:TermGenie GO_REF:0000058 PMID:25049409 down regulation of cytoplasmic transport GOC:TermGenie down-regulation of cytoplasmic transport GOC:TermGenie downregulation of cytoplasmic transport GOC:TermGenie down regulation of cytoplasmic streaming GOC:TermGenie down-regulation of cytoplasmic streaming GOC:TermGenie downregulation of cytoplasmic streaming GOC:TermGenie inhibition of cytoplasmic streaming GOC:TermGenie inhibition of cytoplasmic transport GOC:TermGenie negative regulation of cytoplasmic streaming GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cytoplasmic transport. jl 2014-11-24T13:38:34Z up regulation of cytoplasmic transport up-regulation of cytoplasmic transport upregulation of cytoplasmic transport activation of cytoplasmic streaming activation of cytoplasmic transport positive regulation of cytoplasmic streaming up regulation of cytoplasmic streaming up-regulation of cytoplasmic streaming upregulation of cytoplasmic streaming biological_process GO:1903651 positive regulation of cytoplasmic transport Any process that activates or increases the frequency, rate or extent of cytoplasmic transport. GOC:TermGenie GO_REF:0000058 PMID:25049409 up regulation of cytoplasmic transport GOC:TermGenie up-regulation of cytoplasmic transport GOC:TermGenie upregulation of cytoplasmic transport GOC:TermGenie activation of cytoplasmic streaming GOC:TermGenie activation of cytoplasmic transport GOC:TermGenie positive regulation of cytoplasmic streaming GOC:TermGenie up regulation of cytoplasmic streaming GOC:TermGenie up-regulation of cytoplasmic streaming GOC:TermGenie upregulation of cytoplasmic streaming GOC:TermGenie A process in which a protein is transported to, or maintained in, a location within a vacuolar membrane. mah 2015-01-07T13:15:54Z protein localisation in vacuolar membrane protein localisation to vacuolar membrane protein localization in vacuolar membrane biological_process GO:1903778 protein localization to vacuolar membrane A process in which a protein is transported to, or maintained in, a location within a vacuolar membrane. GOC:TermGenie GO_REF:0000087 PMID:25378562 protein localisation in vacuolar membrane GOC:TermGenie protein localisation to vacuolar membrane GOC:TermGenie protein localization in vacuolar membrane GOC:TermGenie Any process that modulates the frequency, rate or extent of cellular protein localization. jl 2015-01-20T14:32:14Z regulation of cellular protein localisation regulation of channel localizer activity biological_process GO:1903827 regulation of cellular protein localization Any process that modulates the frequency, rate or extent of cellular protein localization. GOC:TermGenie GOC:vw GO_REF:0000058 regulation of cellular protein localisation GOC:TermGenie regulation of channel localizer activity GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cellular protein localization. jl 2015-01-20T14:32:24Z down regulation of cellular protein localisation down regulation of cellular protein localization down-regulation of cellular protein localisation down-regulation of cellular protein localization downregulation of cellular protein localisation downregulation of cellular protein localization negative regulation of cellular protein localisation down regulation of channel localizer activity down-regulation of channel localizer activity downregulation of channel localizer activity inhibition of cellular protein localisation inhibition of cellular protein localization inhibition of channel localizer activity negative regulation of channel localizer activity biological_process GO:1903828 negative regulation of cellular protein localization Any process that stops, prevents or reduces the frequency, rate or extent of cellular protein localization. GOC:TermGenie GOC:vw GO_REF:0000058 down regulation of cellular protein localisation GOC:TermGenie down regulation of cellular protein localization GOC:TermGenie down-regulation of cellular protein localisation GOC:TermGenie down-regulation of cellular protein localization GOC:TermGenie downregulation of cellular protein localisation GOC:TermGenie downregulation of cellular protein localization GOC:TermGenie negative regulation of cellular protein localisation GOC:TermGenie down regulation of channel localizer activity GOC:TermGenie down-regulation of channel localizer activity GOC:TermGenie downregulation of channel localizer activity GOC:TermGenie inhibition of cellular protein localisation GOC:TermGenie inhibition of cellular protein localization GOC:TermGenie inhibition of channel localizer activity GOC:TermGenie negative regulation of channel localizer activity GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cellular protein localization. jl 2015-01-20T14:32:33Z positive regulation of cellular protein localisation up regulation of cellular protein localisation up regulation of cellular protein localization up-regulation of cellular protein localisation up-regulation of cellular protein localization upregulation of cellular protein localisation upregulation of cellular protein localization activation of cellular protein localisation activation of cellular protein localization activation of channel localizer activity positive regulation of channel localizer activity up regulation of channel localizer activity up-regulation of channel localizer activity upregulation of channel localizer activity biological_process GO:1903829 positive regulation of cellular protein localization Any process that activates or increases the frequency, rate or extent of cellular protein localization. GOC:TermGenie GOC:vw GO_REF:0000058 positive regulation of cellular protein localisation GOC:TermGenie up regulation of cellular protein localisation GOC:TermGenie up regulation of cellular protein localization GOC:TermGenie up-regulation of cellular protein localisation GOC:TermGenie up-regulation of cellular protein localization GOC:TermGenie upregulation of cellular protein localisation GOC:TermGenie upregulation of cellular protein localization GOC:TermGenie activation of cellular protein localisation GOC:TermGenie activation of cellular protein localization GOC:TermGenie activation of channel localizer activity GOC:TermGenie positive regulation of channel localizer activity GOC:TermGenie up regulation of channel localizer activity GOC:TermGenie up-regulation of channel localizer activity GOC:TermGenie upregulation of channel localizer activity GOC:TermGenie A process in which a protein is transported to, or maintained in, a location within the nuclear periphery. mah 2013-07-09T13:35:49Z biological_process GO:1990139 protein localization to nuclear periphery A process in which a protein is transported to, or maintained in, a location within the nuclear periphery. GOC:mah PMID:23703609 A process in which a protein is transported to, or maintained in, a location within the nucleoplasm. mah 2013-08-23T15:01:16Z protein localisation to nucleoplasm biological_process GO:1990173 protein localization to nucleoplasm A process in which a protein is transported to, or maintained in, a location within the nucleoplasm. GOC:mah PMID:22918952 protein localisation to nucleoplasm GOC:mah Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process. tanyaberardini 2010-09-15T08:55:45Z regulation of cellular biopolymer biosynthetic process regulation of cellular macromolecule anabolism regulation of cellular macromolecule biosynthesis regulation of cellular macromolecule formation regulation of cellular macromolecule synthesis biological_process GO:2000112 regulation of cellular macromolecule biosynthetic process Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process. GOC:obol regulation of cellular biopolymer biosynthetic process GOC:obol regulation of cellular macromolecule anabolism GOC:obol regulation of cellular macromolecule biosynthesis GOC:obol regulation of cellular macromolecule formation GOC:obol regulation of cellular macromolecule synthesis GOC:obol Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process. tanyaberardini 2010-09-15T08:55:48Z negative regulation of cellular biopolymer biosynthetic process negative regulation of cellular macromolecule anabolism negative regulation of cellular macromolecule biosynthesis negative regulation of cellular macromolecule formation negative regulation of cellular macromolecule synthesis biological_process GO:2000113 negative regulation of cellular macromolecule biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process. GOC:obol negative regulation of cellular biopolymer biosynthetic process GOC:obol negative regulation of cellular macromolecule anabolism GOC:obol negative regulation of cellular macromolecule biosynthesis GOC:obol negative regulation of cellular macromolecule formation GOC:obol negative regulation of cellular macromolecule synthesis GOC:obol Any process that modulates the frequency, rate or extent of RNA biosynthetic process. dph 2011-10-17T11:36:25Z regulation of RNA anabolism regulation of RNA biosynthesis regulation of RNA formation regulation of RNA synthesis biological_process GO:2001141 regulation of RNA biosynthetic process Any process that modulates the frequency, rate or extent of RNA biosynthetic process. GOC:dph regulation of RNA anabolism GOC:obol regulation of RNA biosynthesis GOC:obol regulation of RNA formation GOC:obol regulation of RNA synthesis GOC:obol A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. PATO:0000072 trait quality PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position. quality velocity PATO:0000008 speed A physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position. Wikipedia:http://en.wikipedia.org/wiki/Velocity A scalar optical property that is the intensity, value or amount of perceived light. color intensity color lightness color value quality PATO:0000016 Color brightness refers to the intensity, lightness or value of the light present. Think of this as a dimmer switch. color brightness A scalar optical property that is the intensity, value or amount of perceived light. PATOC:MAH A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. concentration quality PATO:0000033 concentration of A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. Wikipedia:http://en.wikipedia.org/wiki/concentration A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time. quality PATO:0000044 frequency A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time. Wikipedia:http://en.wikipedia.org/wiki/frequency A quality inhering in a bearer by virtue of the bearer's possessing or displaying a distinctive feature in type or degree or effect or force. quality PATO:0000049 intensity A quality inhering in a bearer by virtue of the bearer's possessing or displaying a distinctive feature in type or degree or effect or force. PATOC:GVG A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. quality PATO:0000051 morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATO:0001647 relational shape quality quality PATO:0000052 Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. shape A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's occurrence. PATO:0000156 PATO:0000158 incidence temporal quality PATO:0000057 occurrence quality A quality of a single process inhering in a bearer by virtue of the bearer's occurrence. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. PATO:0000132 PATO:0001565 distribution quality pattern PATO:0000060 spatial pattern A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. PATOC:GVG quality PATO:0000068 TODO: define this or obsolete it and move children somewhere else. qualitative A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. quality PATO:0000069 deviation(from_normal) A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. PATOC:GVG A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. quality PATO:0000117 size A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. WordNet:WordNet A 1-D extent quality which is equal to the distance between two points. quality PATO:0000122 length A 1-D extent quality which is equal to the distance between two points. PATOC:GVG A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. quality PATO:0000125 mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATO:0001032 PATO:0001631 location placement relational spatial quality quality PATO:0000140 position A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATOC:GVG A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATO:0001452 relational structural quality quality PATO:0000141 structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. quality PATO:0000161 rate A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. PATOC:melissa An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. quality PATO:0000169 viability An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. PATOC:GVG A quality of a process which ends earlier than the natural end time or reference process. PATO:0001508 abolished quality incomplete PATO:0000297 TODO: the definition is incorrect. See absent. arrested A quality of a process which ends earlier than the natural end time or reference process. PATOC:LC A speed which is relatively high. high speed quality fast speed PATO:0000303 increased speed A speed which is relatively high. PATOC:GVG A speed which is relatively low. slow slow speed quality PATO:0000304 decreased speed A speed which is relatively low. PATOC:GVG A spatial pattern inhering in a bearer by virtue of the bearer's magnitude of or the relationships between its repeated parts lack consistency. quality PATO:0000330 irregular spatial pattern A spatial pattern inhering in a bearer by virtue of the bearer's magnitude of or the relationships between its repeated parts lack consistency. PATOC:GVG A frequency which is relatively high. high frequency quality frequent PATO:0000380 increased frequency A frequency which is relatively high. PATOC:GVG A frequency which is relatively low. low frequency quality infrequent PATO:0000381 decreased frequency A frequency which is relatively low. PATOC:GVG An intensity which is less than moderate in type or degree or effect or force. quality PATO:0000394 mild An intensity which is less than moderate in type or degree or effect or force. PATOC:GVG An intensity which is extremely bad or unpleasant in type or degree or effect or force. quality PATO:0000396 severe An intensity which is extremely bad or unpleasant in type or degree or effect or force. WordNet:WordNet A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend. bowing quality curled PATO:0000406 curved A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend. WordNet:WordNet A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center. quality round rounded PATO:0000411 circular A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center. thefreedictionary.com:thefreedictionary.com A pattern quality inhering in a bearer by virtue of the bearer's having a repeatable or predictable placement. quality PATO:0000440 regular spatial pattern A pattern quality inhering in a bearer by virtue of the bearer's having a repeatable or predictable placement. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. quality aberrant atypia atypical defective PATO:0000460 abnormal A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. quality average PATO:0000461 normal A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. PATOC:GVG A duration quality of a process which is relatively high. PATO:0000715 high time increased period increased time quality chronic prolonged period slow time PATO:0000498 increased duration A duration quality of a process which is relatively high. PATOC:GVG A duration quality of a process which is relatively low. PATO:0000716 decreased period decreased time low period shortened period quality fast time PATO:0000499 decreased duration A duration quality of a process which is relatively low. PATOC:GVG A quality of a process which starts later than the natural start time or the reference process. quality late PATO:0000502 delayed A quality of a process which starts later than the natural start time or the reference process. PATOC:LC A length quality which is relatively large. long quality PATO:0000573 increased length A length quality which is relatively large. PATOC:GVG A length quality which is relatively small. short quality shortened stubby PATO:0000574 decreased length A length quality which is relatively small. PATOC:GVG A size quality which is relatively high. PATO:0001202 quality big enlarged expanded great large PATO:0000586 increased size A size quality which is relatively high. PATOC:GVG A size quality which is relatively low. hypoplasia underdeveloped quality small tiny PATO:0000587 decreased size A size quality which is relatively low. PATOC:GVG A thickness which is relatively high. high thickness stout thickened quality thick PATO:0000591 increased thickness A thickness which is relatively high. PATOC:GVG A thickness which is relatively low. low thickness quality slender thin PATO:0000592 decreased thickness A thickness which is relatively low. PATOC:GVG A volume which is relatively high. high volume quality large volume PATO:0000595 increased volume A volume which is relatively high. PATOC:GVG A volume which is relatively low. low volume quality small volume PATO:0000596 decreased volume A volume which is relatively low. PATOC:GVG A width which is relatively small. quality narrow PATO:0000599 decreased width A width which is relatively small. PATOC:GVG A width which is relatively large. quality broad wide wide/broad PATO:0000600 increased width A width which is relatively large. PATOC:GVG A symmetry quality inhering in a bearer by virtue of the bearer's lacking symmetry. asymmetric asymmetry quality PATO:0000616 asymmetrical A symmetry quality inhering in a bearer by virtue of the bearer's lacking symmetry. PATOC:GVG A positional quality inhering in a bearer by virtue of the bearer's having two sides; two-sided. quality PATO:0000618 bilateral A positional quality inhering in a bearer by virtue of the bearer's having two sides; two-sided. thefreedictionary.com:thefreedictionary.com A structural quality inhering in a bearer by virtue of the bearer's consisting of blebbing of the nucleus and DNA fragmentation due to the cell undergoing a specific form of programmed cell death termed apoptosis. GO:0006915 quality PATO:0000638 apoptotic A structural quality inhering in a bearer by virtue of the bearer's consisting of blebbing of the nucleus and DNA fragmentation due to the cell undergoing a specific form of programmed cell death termed apoptosis. PATOC:GVG A color brightness which is relatively high. light quality PATO:0000665 high brightness A color brightness which is relatively high. PATOC:MAH A quality of a single process inhering in a bearer by virtue of the bearer's being uninterrupted in time, sequence, substance, or extent. PATO:0000429 uninterrupted quality PATO:0000689 continuous A quality of a single process inhering in a bearer by virtue of the bearer's being uninterrupted in time, sequence, substance, or extent. thefreedictionary.com:thefreedictionary.com A viability quality inhering in a population by virtue of the bearer's long term survival inability. quality PATO:0000718 lethal (sensu genetics) A viability quality inhering in a population by virtue of the bearer's long term survival inability. PATOC:GVG A viability quality inhering in a bearer or a population by virtue of the bearer's ability to survive or the long term survival ability of a given population. quality PATO:0000719 viable A viability quality inhering in a bearer or a population by virtue of the bearer's ability to survive or the long term survival ability of a given population. PATOC:GVG A rate which is relatively low. slow rate quality PATO:0000911 decreased rate A rate which is relatively low. PATO:GVG A rate which is relatively high. fast rate high rate quality PATO:0000912 increased rate A rate which is relatively high. PATO:GVG A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width. quality PATO:0000915 thickness A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width. WordNet:WordNet A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. quality PATO:0000918 volume A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. PATOC:GVG A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite. quality breadth PATO:0000921 This term is for curator easiness - we might consider obsoleting this but we have to consider how curators are going to represent them if we do. width A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's lacking organisation. quality PATO:0000937 disorganized A structural quality inhering in a bearer by virtue of the bearer's lacking organisation. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's having a sharp or tapered end or point. apiculate quality PATO:0000944 sharpness A shape quality inhering in a bearer by virtue of the bearer's having a sharp or tapered end or point. PATOC:GVG A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section. ellipse-shaped ellipsoid elliptical quality oval ovoid PATO:0000947 elliptic A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section. PATOC:GVG A pattern quality of inhering in a bearer by virtue of the correspondence in size, shape, and relative position of the bearer's parts on opposite sides of a dividing line or median plane or about a center or axis. quality PATO:0000965 symmetry A pattern quality of inhering in a bearer by virtue of the correspondence in size, shape, and relative position of the bearer's parts on opposite sides of a dividing line or median plane or about a center or axis. PATOC:GVG A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality quality PATO:0001018 physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width. quality PATO:0001154 elongated A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width. WordNet:WordNet A concentration quality inhering in a bearer by virtue of the bearer's exhibiting concentration. quality PATO:0001159 concentrated A concentration quality inhering in a bearer by virtue of the bearer's exhibiting concentration. PATOC:GVG A concentration which is higher relative to the normal or average. high concentration quality PATO:0001162 increased concentration A concentration which is higher relative to the normal or average. PATOC:GVG A concentration which is lower relative to the normal or average. low concentration quality PATO:0001163 decreased concentration A concentration which is lower relative to the normal or average. PATOC:GVG A quality which inheres in an process. PATO:0001239 PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent quality PATO:0001236 See comments of relational quality of a physical entity. process quality A quality which inheres in an process. PATOC:GVG A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality A quality which inheres in a continuant. PATOC:GVG A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. quality PATO:0001291 electromagnetic (EM) radiation quality A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. quality PATO:0001300 optical quality An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's disposition to varying or changing. quality variability of a physical quality PATO:0001303 variability A quality inhering in a bearer by virtue of the bearer's disposition to varying or changing. Dictionary:http://dictionary.reference.com/ A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATO:0000081 period quality time PATO:0001309 duration quality of a process A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATOC:mellybelly A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent. quality PATO:0001323 area A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent. Wikipedia:http://en.wikipedia.org/wiki/Area A symmetry quality inhering in a bearer by virtue of the bearer's having equal proportion around a central point or axis. quality PATO:0001325 radial symmetry A symmetry quality inhering in a bearer by virtue of the bearer's having equal proportion around a central point or axis. PATOC:GVG A surface feature shape quality inhering in a bearer by virtue of the bearer's having spines, thorns or similar thin projections on its surface. quality PATO:0001365 spiny A surface feature shape quality inhering in a bearer by virtue of the bearer's having spines, thorns or similar thin projections on its surface. PATOC:GVG A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. quality PATO:0001374 ploidy A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. Wikipedia:http://en.wikipedia.org/wiki/Ploidy A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. quality PATO:0001377 polyploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Polyploid A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. quality PATO:0001393 euploid A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Euploid A monadic quality of continuant that exists at the cellular level of organisation. quality PATO:0001396 cellular quality A monadic quality of continuant that exists at the cellular level of organisation. PATOC:GVG A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. quality PATO:0001404 nucleate quality A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. PATOC:GVG A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. quality PATO:0001406 binucleate A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. Biology-online:Biology-online A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. quality PATO:0001407 mononucleate A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. Biology-online:Biology-online A shape quality inhering in a bearer by virtue of the bearer's terminating in a point or edge. quality PATO:0001419 sharp A shape quality inhering in a bearer by virtue of the bearer's terminating in a point or edge. PATOC:GVG A structural quality inhering in a bearer by virtue of whether the bearer includes all its components. quality PATO:0001442 wholeness A structural quality inhering in a bearer by virtue of whether the bearer includes all its components. thefreedictionary.com:thefreedictionary.com A broken quality inhering in a bearer by virtue of the bearer's being broken open. PATO:0001443 PATO:0001820 burst fractured fragmented ruptured quality cracked hemorrhaged split torn PATO:0001444 broken A broken quality inhering in a bearer by virtue of the bearer's being broken open. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being gradually narrower or thinner toward one end. taper quality PATO:0001500 tapered A shape quality inhering in a bearer by virtue of the bearer's being gradually narrower or thinner toward one end. WordNet:WordNet A pattern inhering in a surface by virtue of the bearer's being marked by the presence of dots, punctures, points or pits. quality dotted spotted stippled PATO:0001512 punctate A pattern inhering in a surface by virtue of the bearer's being marked by the presence of dots, punctures, points or pits. medical-dictionary:medical-dictionary The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. OBO_REL:has_part extra or missing physical or functional parts has or lacks parts of type mereological quality number of quality cardinality number PATO:0001555 has number of The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. PATOC:CJM A quality of a process inhering in a bearer by virtue of the bearer's lacking a processual part as specified by the additional entity. quality PATO:0001558 lacking processual parts A quality of a process inhering in a bearer by virtue of the bearer's lacking a processual part as specified by the additional entity. PATOC:GVG A mass which is lower than normal or average. PATO:0000579 low mass small mass quality PATO:0001562 decreased mass A mass which is lower than normal or average. PATO:GVG A mass which is higher than normal or average. PATO:0000578 high mass large mass quality PATO:0001563 increased mass A mass which is higher than normal or average. PATO:GVG A quality of a process inhering in a bearer by virtue of the bearer's processual parts. quality PATO:0001564 extra or missing processual parts A quality of a process inhering in a bearer by virtue of the bearer's processual parts. PATOC:GVG A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending. quality PATO:0001591 curvature A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending. WordNet:WordNet A morphological quality inhering in a bearer by virtue of the bearer's being distorted in form. quality disfigured distorted PATO:0001617 deformed A morphological quality inhering in a bearer by virtue of the bearer's being distorted in form. thefreedictionary.com:thefreedictionary.com A spatial pattern inhering in a bearer by virtue of the bearer's being gathered or tending to gather into a mass or whole. clustered quality PATO:0001629 aggregated A spatial pattern inhering in a bearer by virtue of the bearer's being gathered or tending to gather into a mass or whole. WordNet:WordNet A positional quality inhering in a bearer by virtue of the bearer's being distributed or spread over a considerable extent. quality PATO:0001630 dispersed A positional quality inhering in a bearer by virtue of the bearer's being distributed or spread over a considerable extent. WordNet:WordNet A size quality inhering in a bearer by virtue of the bearer's having a short, stocky build. quality PATO:0001643 stubby A size quality inhering in a bearer by virtue of the bearer's having a short, stocky build. thefreedictionary.com:thefreedictionary.com A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. 1-D size quality PATO:0001708 1-D extent A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. PATOC:GVG A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions. 2-D size quality PATO:0001709 2-D extent A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions. PATOC:GVG A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. 3D size quality PATO:0001710 3-D extent A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. PATOC:GVG A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. quality PATO:0001739 radiation quality A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's being extended on all sides of another entity simultaneously. encircling quality PATO:0001772 surrounding A spatial quality inhering in a bearer by virtue of the bearer's being extended on all sides of another entity simultaneously. thefreedictionary.com:thefreedictionary.com A shape quality inhering in a bearer by virtue of the bearer's having three angles. deltoid quality triangle triangle-shaped PATO:0001875 triangular A shape quality inhering in a bearer by virtue of the bearer's having three angles. wordreference:wordreference A shape quality inhering in a bearer by virtue of the bearer's consisting of two curves, in opposite directions. S-shaped. S-shaped sigmoidal quality PATO:0001878 sigmoid A shape quality inhering in a bearer by virtue of the bearer's consisting of two curves, in opposite directions. S-shaped. PATOC:CJM A shape quality inhering in a bearer by virtue of the bearer's forming two equal obtuse triangles with a short side in common. sagittate quality PATO:0001881 Gradually enlarged at the base, like the head of an arrow. arrow-shaped A shape quality inhering in a bearer by virtue of the bearer's forming two equal obtuse triangles with a short side in common. ISBN:0881923214 RKC:RKC A physical quality inhering in a bearer by virtue of the bearer's participation in movement. quality PATO:0001906 movement quality A physical quality inhering in a bearer by virtue of the bearer's participation in movement. PATOC:GVG A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. quality PATO:0001908 multinucleate A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. PATOC:GVG A surface shape quality inhering in a bearer by virtue of the bearer's shape of features present on its surface or outer shell. quality PATO:0001925 This quality either inheres directly in the surface, or in the entity that has the surface. For example, to say that a particular fly wing is curved is shorthand for saying the wing has a surface which is curved. surface feature shape A surface shape quality inhering in a bearer by virtue of the bearer's shape of features present on its surface or outer shell. PATOC:CJM A variability quality inhering in a bearer by virtue of whether the bearer exhibits shape variation or change. quality PATO:0001929 variability of shape A variability quality inhering in a bearer by virtue of whether the bearer exhibits shape variation or change. PATOC:GVG A variability quality inhering in a bearer by virtue of whether the bearer exhibits size variation or change. quality PATO:0001956 variability of size A variability quality inhering in a bearer by virtue of whether the bearer exhibits size variation or change. PATOC:GVG A variability of size which is relatively high. high variability of size quality PATO:0001958 increased variability of size A variability of size which is relatively high. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being partly divided into a determinate number of regions. quality PATO:0001979 lobed A shape quality inhering in a bearer by virtue of the bearer's being partly divided into a determinate number of regions. ISBN:0881923214 A quality that inheres in an entire organism or part of an organism. quality PATO:0001995 organismal quality A quality that inheres in an entire organism or part of an organism. PATOC:CJM The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type. loss of quality PATO:0001999 lacks parts or has fewer parts of type The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type. PATOC:CJM A quality of physical entities inhering in a bearer by virtue of the bearer's lacking a physical part as specified by the additional entity. PATO:0001557 OBO_REL:lacks_part lacks all physical parts of type quality PATO:0002000 Example: [E=organism Q=lacks_all_parts_of_type E2=Wing] - applies to an organism. A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e that has no wings, where wings are normally present in that organism type. In OWL this is equivalent to a restriction on the OBO_REL:has_part relation with cardinality=0, i.e has_part 0 E2. lacks all parts of type A quality of physical entities inhering in a bearer by virtue of the bearer's lacking a physical part as specified by the additional entity. PATOC:CJM The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. PATO:0001569 decreased number of has decreased number of has fewer physical parts of type quality PATO:0002001 Example: [E=hand Q=has_fewer_parts_of_type E2=digit] - applies to an organism that has no less fingers than is normal for organisms of that type. has fewer parts of type The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. PATOC:CJM The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. PATO:0001560 has extra parts of has increased number of having extra physical parts having supernumerary physical parts increased number of quality PATO:0002002 In polydactyly, the bearer of the quality is the hand, and the entity type being counted is 'finger'. In EQ syntax, E=hand, Q=<this> E2=finger. has extra parts of type The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. PATOC:CJM A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. quality 2-D projection cross-sectional PATO:0002006 2-D shape A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. PATOC:CJM An occurrence which is relatively high. George Gkoutos 2009-03-26T11:10:11Z increased incidence quality PATO:0002051 increased occurrence An occurrence which is relatively high. PATOC:GVG An occurrence which is relatively low. George Gkoutos 2009-03-26T11:12:35Z decreased incidence quality PATO:0002052 decreased occurrence An occurrence which is relatively low. PATOC:GVG An area which is relatively high. George Gkoutos 2009-03-30T04:11:43Z quality PATO:0002057 increased area An area which is relatively high. PATOC:GVG An area which is relatively low. George Gkoutos 2009-03-30T04:12:11Z quality PATO:0002058 decreased area An area which is relatively low. PATOC:GVG george 2009-06-05T09:16:46Z quality PATO:0002062 physical quality of a process A shape quality inhering in a bearer by virtue of the bearer's being arranged like rays or radii; radiating from a common center. George Gkoutos 2009-07-01T01:48:19Z stellate quality PATO:0002065 star shaped A shape quality inhering in a bearer by virtue of the bearer's being arranged like rays or radii; radiating from a common center. PATOC:me Having extra or fewer parts. George Gkoutos 2009-09-21T10:41:58Z quality PATO:0002083 altered number of Having extra or fewer parts. PATOC:GVG A positional quality inhering in a bearer by virtue of the bearer's being at the edge or boundary of a related entity. george 2009-10-05T02:58:16Z quality PATO:0002107 peripheral A positional quality inhering in a bearer by virtue of the bearer's being at the edge or boundary of a related entity. PATOC:GVG A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. George Gkoutos 2010-03-10T03:18:15Z PATO:0002061 relational molecular quality quality PATO:0002182 molecular quality A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. PATOC:GVG A lobed quality inhering in a bearer by virtue of the bearer's being divided into or having two lobes. george 2010-07-08T01:54:08Z quality PATO:0002214 bilobed A lobed quality inhering in a bearer by virtue of the bearer's being divided into or having two lobes. thefreedictionary:http://www.thefreedictionary.com/bilobed A quality inhering in a bearer that is shaped in the form of a fan. george 2010-07-09T01:43:42Z fan-like quality PATO:0002219 fan-shaped A quality inhering in a bearer that is shaped in the form of a fan. thefreedictionary:http://www.thefreedictionary.com/fan-shaped A structural quality inhering in a bearer by virtue of the bearer's being arranged in a systematic fashion. george 2010-09-16T10:22:52Z quality PATO:0002264 organization quality A structural quality inhering in a bearer by virtue of the bearer's being arranged in a systematic fashion. PATOC:GVG A positional quality inhering in a bearer by virtue of the bearer's being located in a position equidistant from edges. george 2010-10-05T01:09:32Z quality PATO:0002268 centered A positional quality inhering in a bearer by virtue of the bearer's being located in a position equidistant from edges. PATOC:OREGON A quality that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:39:43Z quality PATO:0002300 increased quality A quality that has a value that is increased compared to normal or average. PATOC:GVG A quality that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:40:15Z quality PATO:0002301 decreased quality A quality that has a value that is decreased compared to normal or average. PATOC:GVG A quality of a process that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:50:59Z quality PATO:0002302 decreased process quality A quality of a process that has a value that is decreased compared to normal or average. PATOC:GVG A quality of an object that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:51:54Z quality PATO:0002303 decreased object quality A quality of an object that has a value that is decreased compared to normal or average. PATOC:GVG A quality of a process that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:53:08Z quality PATO:0002304 increased process quality A quality of a process that has a value that is increased compared to normal or average. PATOC:GVG A quality of an object that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:54:01Z quality PATO:0002305 increased object quality A quality of an object that has a value that is increased compared to normal or average. PATOC:GVG A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt George Gkoutos 2011-10-12T12:45:16Z Lamé curve quality PATO:0002318 superelliptic A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt wiktionary:superellipse A temporal distribution pattern of process occurrences within a regulation/reference process. George Gkoutos 2011-11-22T01:12:28Z quality PATO:0002323 temporal distribution quality A temporal distribution pattern of process occurrences within a regulation/reference process. PATOC:LC The temporal relation between the end of the process with respect to a reference process. George Gkoutos 2011-11-23T11:46:00Z quality PATO:0002324 offset quality The temporal relation between the end of the process with respect to a reference process. PATOC:LC The temporal relation between the start of the process with respect to a reference process. George Gkoutos 2011-11-23T11:47:34Z quality PATO:0002325 onset quality The temporal relation between the start of the process with respect to a reference process. PATOC:LC A quality inhering in a bearer by virtue of the bearer's length being notably lower than its width. gkoutos 2012-04-18T06:31:29Z quality PATO:0002364 shortened A quality inhering in a bearer by virtue of the bearer's length being notably lower than its width. PATOC:GVG Having a shape that resembles a many-lobed "berry," such as a raspberry. gkoutos 2012-07-05T14:58:05Z quality PATO:0002378 acinus Having a shape that resembles a many-lobed "berry," such as a raspberry. wikipedia:https://en.wikipedia.org/wiki/Acinus A quality that that inheres in a population of cells CMPO:0000002 cell population phenotype cell population phenotype A quality that inheres in or specifically depends on a cellular process, a cell population, a whole cell or a subcellular structure. CMPO:0000003 cellular phenotype cellular phenotype A collection of qualities that inhere in the whole cell relating to the cell's shape, size or structure CMPO:0000005 cell morphology phenotype cell morphology A quality that inheres in a cellular process cell physiology phenotype CMPO:0000007 cell process phenotype cell process phenotype An increase or decrease in the number of specified components within a cell CMPO:0000008 cell component number phenotype cell component number A collection of size qualities that inhere in a cellular component CMPO:0000010 cell component size phenotype cell component size A collection of shape qualities that inhere in a cellular component CMPO:0000011 cell component shape phenotype cell component shape A collection of structure qualities that inhere in a cellular component CMPO:0000012 cell component structure phenotype cell component structure A phenotype relating to the ability of a cell survive or to develop normally CMPO:0000013 cell viability phenotype cell viability A cell phenotype where the cell is viable CMPO:0000014 viable cell phenotype viable cell A cell phenotype where the cell is not viable CMPO:0000015 inviable cell phenotype inviable cell A nucleation quality that inheres in the whole cell CMPO:0000016 cell nucleation phenotype cell nucleation CMPO:0000017 mononuclear cell phenotype mononuclear cell A multinucleate quality that inheres in a cell polynuclear cell CMPO:0000018 multinucleated cell phenotype multinucleated cell A collection of qualities that inhere in any constituent part of the cytoskeleton, a cellular scaffolding or skeleton that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (e.g. the movement of vesicles and organelles) and cellular division. Includes constituent parts of intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice. CMPO:0000020 cytoskeletal phenotype cytoskeletal phenotype A collection of qualities that inhere in any constituent part of the endoplasmic reticulum, the irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. CMPO:0000021 endoplasmic reticulum phenotype endoplasmic reticulum phenotype A collection of qualities that inhere in any constituent part of the Golgi apparatus, a compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack CMPO:0000022 golgi phenotype golgi phenotype A collection of qualities that inhere in any constituent part of a mitochondrion, a semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. mitochondrial part phenotype CMPO:0000023 mitochondrion phenotype mitochondrion phenotype A collection of qualities that inhere in any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. CMPO:0000024 nuclear phenotype nuclear phenotype A collection of qualities that inhere in a cellular organelle relating to the organelle's shape CMPO:0000026 organelle shape phenotype organelle shape A collection of qualities that inhere in the nucleus relating to the ratios of distances between its features (points, edges, surfaces and also holes etc). nuclear shape CMPO:0000027 nucleus shape phenotype A phenotype where the attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules is observed CMPO:0000028 cell adhesion phenotype cell adhesion phenotype A collection of qualities that inhere the cell cycle CMPO:0000029 cell cycle phenotype cell cycle phenotype A phenotype where the cell death process process is observed PMID:20360735 CMPO:0000030 cell death phenotype cell death phenotype A phenotype observation of a process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. CMPO:0000032 cell membrane organisation phenotype cell membrane organisation phenotype A phenotype of a cell involving its translation from one location to another PMID:20360735 CMPO:0000033 cell migration phenotype cell migration phenotype A phenotype observation of the process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. CMPO:0000035 cell growth phenotype cell growth phenotype A phenotype observation of the process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the alignment of chromosomes at the metaphase plate, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. CMPO:0000036 chromosome segregation phenotype chromosome segregation phenotype A phenotype observation of chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. CMPO:0000037 metabolic process phenotype metabolic process phenotype A phenotype observations where any process in which an organelle is transported to, and/or maintained in, a specific location. CMPO:0000038 organelle localization phenotype organelle localization phenotype A phenotype observation where a process modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. CMPO:0000039 regulation of metabolic process phenotype regulation of metabolic process phenotype A phenotype observation of a process that modulates the frequency, rate or extent of signal transduction. CMPO:0000040 regulation of signal transduction phenotype regulation of signal transduction phenotype A phenotype observation of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. CMPO:0000041 transport phenotype transport phenotype An increased number of specified cellular components relative to normal CMPO:0000042 increased cell component number phenotype increased cell component number A decrease in number of specified cellular components relative to normal CMPO:0000043 decreased cell component number phenotype decreased cell component number A phenotype observation where the cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments. apoptotic DNA CMPO:0000047 apoptotic DNA fragmentation phenotype apoptotic DNA fragmentation A phenotype observation at the level of the cell shape where the cell is apoptotic CMPO:0000048 dispersed outline with blobby protrusions apoptotic cell shape phenotype apoptotic cell shape Groups of cells gathered or tending to gather into a mass or whole. aggregated cells cell aggregates cell islands clustered cells CMPO:0000049 aggregated cells in population aggregated cells in population Number of cells in a population phenotype CMPO:0000050 altered cell number in population cell number in population The population has an increased number of cells with respect to normal CMPO:0000051 increased cell numbers increased cell numbers The population has a decreased number of cells with respect to normal decreased cells fewer cells less cells reduced cell numbers CMPO:0000052 decreased cell numbers decreased cell numbers increased number of cells in S phase mitosis CMPO:0000053 more cells in S A population of cells where a specifcied biological process is occuring or is observed. CMPO:0000054 cell population phenotype by process cell population process increased cell numbers in G1 CMPO:0000055 more cells in G1 increased number of cells in G2M increased mitotic index CMPO:0000056 more cells in G2M decreased number of cells in G1 phase less cells in G1 CMPO:0000057 fewer cells in G1 decreased number of cells in G2M phase decreased mitotic index less cells in G2M CMPO:0000058 fewer cells in G2M decreased number of cells in S phase decreased number of cells in S less cells in S CMPO:0000059 fewer cells in S A phenotype observation at the level of focal adhesions where the components number has decreased. decreased focal adhesion abundance CMPO:0000063 decreased number of focal adhesion phenotype decreased number of focal adhesion A phenotype observation where the focal adhesion is located in a position equidistant from the edges of the cell PMID:19667130 CMPO:0000064 centrally located focal adhesion phenotype centrally located focal adhesion A phenotype observation at the level of a cellular component relating to the components position in the cell CMPO:0000065 cell component position phenotype cell component position A phenotype observation where the focal adhesions's position is at the edge or boundary of a related entity. PMID:19667130 CMPO:0000066 peripheral focal adhesion phenotype peripheral focal adhesion A phenotype observation at the level of filopodia where the components number has decreased. fewer filopodia CMPO:0000067 decreased number of filopodia phenotype decreased number of filopodia A phenotype observation at the level of microtubules where the components number has decreased. fewer microtubules CMPO:0000068 decreased number of microtubules phenotype decreased number of microtubules A phenotype observation at the level of dendritic branches where the components number has decreased. CMPO:0000069 decreased number of dendritic branches phenotyope Single cell with protrusions PMID:20531400 cell with protrusions CMPO:0000071 cell with projections An increase in number of any cell projection relative to normal CMPO:0000072 increased number of cell projections phenotype increased number of cell projections increased number of cells in population with projections CMPO:0000073 more cells with projections A phenotype observation at the level of cell projections where the components number has decreased. CMPO:0000074 decreased number of cell projections phenotype decreased number of cell projections decreased number of cells in population with projections CMPO:0000075 fewer cells with projections A phenotype observation at the level of filopodia where the components number has increased. more filopodia CMPO:0000076 increased number of filopodia A phenotype observation at the level of the cell shape where the cell is elongated, with a length notably greater than its width bipolar cell CMPO:0000077 elongated cell phenotype elongated cell Cells in population with a length notably greater than their width PMID:21893601; PMID:20531400 CMPO:0000078 elongated cells in population elongated cells in population A phenotype observation at the level of lamellipodia where the components number has increased. lamellipodium phenotype CMPO:0000080 increased number of lamellipodia phenotype increased number of lamellipodia A phenotype observation at the level of lamellipodia where the components number has decreased. CMPO:0000081 decreased number of lamellipodia phenotype decreased number of lamellipodia increased lamellipodia cells in population phenotype CMPO:0000083 more lamellipodia cells decreased lamellipodia cells in population phenotype CMPO:0000084 fewer lamellipodia cells A phenotype observation at the level of the whole cell relating to the cell's ploidy CMPO:0000085 cell ploidy phenotype cell ploidy A cell phenotype with more than two homologous sets of chromosomes. CMPO:0000086 polyploid cell phenotype polyploid cell A phenotype observation at the level of athe S phase of the mitotic cell cycle CMPO:0000087 S phase mitotic phenotype S phase mitotic phenotype A phenotype observation at the level of a G1 phase of the mitotic cell cycle CMPO:0000088 G1 phase mitotic phenotype G1 phase mitotic phenotype A phenotype observation at the level of the G2/M transition of the mitotic cell cycle CMPO:0000089 G2/M transition phenotype G2/M transition phenotype A phenotype observation at the level of a cell cycle phase CMPO:0000090 cell cycle phase phenotype cell cycle phase phenotype increased number of polyploid cells in population CMPO:0000091 more polyploid cells A phenotype observation at the level of focal adhesions where the components number has increased. increased focal adhesion abundance CMPO:0000092 increased number of focal adhesion phenotype increased number of focal adhesion A phenotype observation at the level of nucleoli where the components number has increased. CMPO:0000093 increased number of nucleoli phenotype increased number of nucleoli A phenotype observation at the level of nucleoli where the components number has decreased. CMPO:0000094 decreased number of nucleoli phenotype decreased number of nucleoli more cells with decreased number of nucleoli CMPO:0000095 more cells with decreased number of nucleoli increased number of nucleoli in population phenotype CMPO:0000096 more cells with increased number of nucleoli A phenotype observation at the level of microtubules where the components number has increased. more microtubules CMPO:0000097 increased number of microtubules phenotype increased number of microtubules A phenotype observation at the level of the phagosomes, a membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis. phagosomes present phenotype CMPO:0000102 phagosomes phenotype phagosomes A phenotype observation where phagosomes are absent CMPO:0000103 phagosomes absent phenotype phagosomes absent A phenotype observation at the level of the actin filaments, a filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. CMPO:0000104 actin filament phenotype actin filament phenotype A phenotype observation at the level of actin filaments where the components number has increased. PMID: 21893601 PMID:20531400 actin fiber cells more actin more total actin CMPO:0000105 increased number of actin filament phenotype increased number of actin filament A phenotype observation at the level of actin filaments where the components number has decreased. PMID: 21893601 less actin less total actin CMPO:0000106 decreased number of actin filament phenotype decreased number of actin filament increased number of actin filament cells in population CMPO:0000107 more actin filament cells decreased number of actin filament phenotypes in population decreased number of actin filament cells CMPO:0000108 fewer actin filament cells A phenotype observation where the cytoskeleton is located in a position equidistant from the edges of the cell CMPO:0000109 centered cytoskeleton phenotype centered cytoskeleton A phenotype observation where the nucleus is located in a position equidistant from the edges of the cell CMPO:0000110 centered nucleus phenotype centered nucleus A phenotype observation where the nucleus is distributed or spread over a considerable extent. CMPO:0000111 dispersed nucleus phenotype dispersed nucleus A phenotype observation at the level of nucleus consisting of blebbing of the nucleus and DNA fragmentation due to the cell undergoing a specific form of programmed cell death termed apoptosis. CMPO:0000112 apoptopic nucleus phenotype apoptopic nucleus A phenotype observation where the nucleus is distorted in form CMPO:0000113 deformed nucleus A phenotype observation where the nucleus's position is at the edge or boundary of a related entity. CMPO:0000114 peripheral nucleus phenotype peripheral nucleus A phenotype observation where the cytoskeleton's position is at the edge or boundary of a related entity. CMPO:0000115 peripheral cytoskeleton phenotype peripheral cytoskeleton A phenotype observation at the level of the cell shape where the shape is abnormal CMPO:0000116 abnormal cell shape phenotype abnormal cell shape A lobed quality inhering in a nucleus by virtue of the nucleus being divided into or having two lobes. bilobed CMPO:0000117 bilobed nucleus phenotype bilobed nucleus A phenotype observation at the level of the cell shape where the cell is round PMID:21893601 circular cell low eccentricity cell spherical cell CMPO:0000118 not spreading cell round cell phenotype round cell A phenotype observation of the length of the focal adhesion is notably higher than the width. long focal adhesion CMPO:0000119 elongated focal adhesion A phenotype observation of the length of the nucleus is notably higher than the width. long nucleus CMPO:0000120 elongated nucleus A phenotype observation at the level of the cell shape where the cell is arrow shaped, with a wide front and a sharp tail, displaying monopolar cell growth triangular shaped cell CMPO:0000121 arrow shaped cell phenotype A phenotype observation at the level of the cell shape where the cell has a triangular shape, with a wide front and a sharp tail, displaying cell motility arrow shaped cell CMPO:0000122 triangular shaped cell phenotype triangular shaped cell A phenotype observation where the shape of the nucleus has every part of the surface or the circumference equidistant from the center. circular nucleus round nucleus CMPO:0000123 round nucleus phenotype round nucleus A phenotype observation at the level of the nuclear body, an extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. CMPO:0000125 nuclear body phenotype nuclear body A phenotype observation where the nuclear body size is relatively high. PMID:22884692 CMPO:0000126 increased nuclear body size phenotype increased nuclear body size A phenotype observation where the nuclear body size is relatively low. PMID:22884692 CMPO:0000127 decreased nuclear body size phenotype decreased nuclear body size A phenotype observation at the level of the cell size where a cell is larger with respect to normal/wild-type PMID:20531400 big cell increased cell area large cell CMPO:0000128 increased cell size phenotype increased cell size A phenotype observation at the level of the cell size where a cell is smaller with respect to normal/wild-type small cell CMPO:0000129 decreased cell size phenotype A phenotype observation at the level of the golgi where the golgi's volume has decreased. CMPO:0000130 decreased golgi volume phenotype decreased golgi volume A phenotype observation at the level of the golgi where the golgi's volume has increased. CMPO:0000131 increased golgi volume phenotype increased golgi volume A phenotype observation at the level of a cilium where the components length has decreased. CMPO:0000132 decreased cilium length phenotype decreased cilium length A phenotype observation at the level of a cilium where the components length has increased. CMPO:0000133 increased cilium length phenotype increased cilium length A phenotype observation where the size of the focal adhesion has decreased. CMPO:0000134 decreased size of focal adhesion phenotype decreased size of focal adhesion A phenotype observation where the size of the focal adhesion has increased. CMPO:0000135 increased size of focal adhesion phenotype increased size of focal adhesion A phenotype observation where the area of the focal adhesion has decreased. pmid:19667130 small focal adhesion CMPO:0000136 decreased focal adhesion area phenotype decreased focal adhesion area A phenotype observation where the area of the focal adhesion has increased. pmid:19667130 large focal adhesion CMPO:0000137 increased focal adhesion area phenotype increased focal adhesion area A phenotype observation where the length of the focal adhesion has decreased. pmid:19667130 short focal adhesion CMPO:0000138 decreased focal adhesion length phenotype decreased focal adhesion length A phenotype observation where the length of the focal adhesion has increased. CMPO:0000139 increased focal adhesion length phenotype increased focal adhesion length A phenotype observation where the size of the nucleus has increased PMID:20360735 PMID:20531400 increased DNA area large nuclei large nucleus CMPO:0000140 increased nucleus size phenotype increased nucleus size A phenotype observation where the size of the nucleus has decreased PMID:20360735 PMID:21893601 decreased DNA area small nucleus CMPO:0000141 decreased nucleus size phenotype decreased nucleus size A phenotype of a cell that has both an increased nuclei size phenotypes and a G1 phase phenotype CMPO:0000143 increased nuclei size in G1 phenotype increased nuclei size in G1 A phenotype of a cell that has both a decreased nuclei size phenotypes and a G1 phase phenotype small nuclei in G1 CMPO:0000144 decreased nuclei size in G1 phenotype decreased nuclei size in G1 A phenotype observation where the thickness of the dendritic branches has increased. CMPO:0000145 increased thickness of dendritic branches phenotype increased thickness of dendritic branches A phenotype observation where the thickness of the dendritic branches has decreased. CMPO:0000146 decreased thickness of dendritic branches A phenotype observation where the microtublue structure is disorganised pmid:21893601 microtubule disorganised CMPO:0000147 disorganized microtubules phenotype disorganized microtubules A phenotype observation at the level of podosomes, an actin-rich adhesion structure characterized by formation upon cell substrate contact and localization at the substrate-attached part of the cell. CMPO:0000148 podosome phenotype podosome A phenotype observation where the cytoskeleton is symmetric, having equal proportions around a central point or axis. CMPO:0000149 radial cytoskeleton phenotype radial cytoskeleton Phenotype observation organised by specific named organelles. CMPO:0000150 organelle phenotype A phenotype observation where the structure of the endoplasmic reticulum is fragmented or broken. broken endoplasmic reticulum CMPO:0000151 fragmented endoplasmic reticulum phenotype fragmented endoplasmic reticulum A phenotype observation at the level of the golgi where the golgi's structure is broken broken golgi broken golgi phenotype CMPO:0000152 fragmented golgi phenotype fragmented golgi A phenotype observation where the structure of the mitochondria is fragmented or broken. broken mitochondria CMPO:0000153 fragmented mitochondria phenotype fragmented mitochondria A phenotype observation where the nuclear's color brightness is relatively high. PMID:20531400 CMPO:0000154 bright nuclei phenotype bright nuclei A phenotype observation where the structure of the nucleus is fragmented or broken. broken nucleus CMPO:0000155 fragmented nucleus phenotype fragmented nucleus A phenotype observation where nuclear envelopes form around single chromosomes or small sets of chromosomes. Forming a grape like structure pmid:20360735 grape CMPO:0000156 Mitocheck Publication: http://www.ncbi.nlm.nih.gov/pubmed/20360735 Micronucleation, i.e. presumably nuclear envelopes around single chromosomes or small sets of chromosomes. graped micronucleus phenotype graped micronucleus A phenotype observation where the shape of the nucleus is abnormal PMID:20360735 abnormal nuclear shape strange nuclear shape CMPO:0000157 abnormal nucleus shape phenotype A phenotype observation at the level of the G2/M transition of the mitotic cell cycle where the nuclei are decreased in size with respect to normal CMPO:0000158 decreased nuclei size in G2/M phenotype decreased nuclei size in G2/M A phenotype observation at the level of a cellular component where the cell component is absent CMPO:0000159 absence of cellular component phenotype absence of cellular component A phenotype of a cell population relating to the ability of the cells to live and develop normally CMPO:0000160 cell population viability phenotype cell viability in population phenotype increased number of viable cell phenotype in a population CMPO:0000161 increased cell viability in population increased cell viability in population decreased number of viable cell phenotype in a population CMPO:0000162 decreased cell viability in population decreased cell viability in population A population phenotype relating to the size, shape or structure of the cells within a population CMPO:0000163 cell population phenotype by morphology cell population morphology A phenotype that results in the absence of cytokinesis CMPO:0000164 absence of cytokinesis phenotype absence of cytokinesis A phenotype observation at the level of cytokinesis CMPO:0000165 cytokinesis phenotype cytokinesis phenotype A phenotype observation of the process resulting in the physical partitioning and separation of a cell into daughter cells. CMPO:0000166 cell division phenotype cell division phenotype A phenotype where the cell division process occurs at a higher rate faster cell division CMPO:0000168 increased rate of cell division phenotype increased rate of cell division A phenotype where the cell division process occurs at a lower rate slower cell division CMPO:0000169 decreased rate of cell division phenotype decreased rate of cell division A phenotype observation of the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence. CMPO:0000170 telomerase activity phenotype telomerase activity phenotype A phenotype observation where the occurane of telomerase activity is decreased CMPO:0000171 decreased telomerase activity phenotype decreased telomerase activity A phenotype observation where the occurane of telomerase activity is increased CMPO:0000172 increased telomerase activity phenotype increased telomerase activity A phenotype of a cell that is arrested at the G0/1 transition CMPO:0000173 (from GO) Under certain conditions, cells exit the cell cycle during G1 and remain in the G0 state as nongrowing, non-dividing (quiescent) cells. G0/1 arrested phenotype G0/1 arrested A phenotype observation where the endoplasmic reticulum is oriented in the cell with extremities at either end of the main axis. polarized endoplasmic reticulum CMPO:0000174 polarized endoplasmic reticulum phenotype polarized endoplasmic reticulum A quality that inheres in a molecular component of a cell CMPO:0000175 molecular component phenotype molecular component phenotype A phenotype observation at the level of the cell DNA CMPO:0000176 cell DNA phenotype cell DNA phenotype A shape quality that inheres in a DNA molecule where the shape of the molecule is abnormal. CMPO:0000177 This phenotype often results in a nucleus with an irregular shape phenotype. misshapen DNA A phenotype observation at the level of the site of double-strand break, a region of a chromosome at which a DNA double-strand break has occurred. CMPO:0000180 site of double-strand break phenotype site of double-strand break A phenotype observation at the level of double strand breaks where the components number has decreased. CMPO:0000181 decreased number of site of double-strand break phenotype decreased number of site of double-strand break A phenotype observation where the number of double-strand breaks has increased CMPO:0000182 increased number of site of double-strand break phenotype increased number of site of double-strand break CMPO:0000185 cell-matrix adhesion phenotype cell-matrix adhesion phenotype A phenotype observation at the level of a cellular component where the components size has increased. CMPO:0000186 increased cell component size phenotype increased cell component size A phenotype observation at the level of a cellular component where the components size has decreased. CMPO:0000187 decreased cell component size phenotype decreased cell component size A phenotype observation where the morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate. substrate adhesion-dependent cell spreading phenotype CMPO:0000188 cell spreading phenotype cell spreading phenotype A phenotype observation of a biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. CMPO:0000189 cellular development phenotype cellular development phenotype A phenotype observation at the level of axons where the components number has decreased. CMPO:0000190 decreased number of axons phenotype decreased number of axons A phenotype observation at the level of axons where the components number has increased. CMPO:0000191 increased number of axons phenotype increased number of axons A phenotype observation at the level of the mitotic cell cycle CMPO:0000194 mitotic process phenotype mitotic process phenotype A phenotype of a cell where a particular process is arrested, or ends earlier in time than expected CMPO:0000195 arrested process phenotype arrested process A phenotype of a cell where the M phase of mitotic cell cycle process is arrested, or ends earlier in time than expected m phase arrest mitosis incomplete process phenotype mitotic arrest CMPO:0000196 M phase arrested phenotype M phase arrested A phenotype observation where mitosis is delayed PMID:20360735 Mitotic delay CMPO:0000202 mitosis delayed phenotype mitosis delayed A phenotype of a cell is arrested in G2 pahse of the cell cycle. CMPO:0000203 G2 arrested phenotype G2 arrested A phenotype of a cell where the S phase process is arrested, or ends earlier in time than expected CMPO:0000204 S phase arrested phenotype S phase arrested A phenotype observation where the duration of the exit from mitosis is increased PMID:20711181 prolonged mitotic exit CMPO:0000205 increased duration of exit from mitosis phenotype increased duration of exit from mitosis CMPO:0000206 decreased duration of exit from mitosis phenotype decreased duration of exit from mitosis A phenotype observation at the level of a G2 phase of the mitotic cell cycle CMPO:0000207 G2 phase mitotic phenotype G2 phase mitotic phenotype A phenotype observation at the level of the mitotic metaphase of the cell cycle CMPO:0000208 mitotic metaphase phenotype mitotic metaphase phenotype increased number of mitotic metaphase cells in population phenotype CMPO:0000210 more mitotic metaphase cells decreased number of mitotic metaphase cells in population phenotype CMPO:0000211 fewer mitotic metaphase cells A phenotype where the cell cycle is in some way abnormal altered level of protein in cell nucleus CMPO:0000212 abnormal cell cycle phenotype abnormal cell cycle A phenotype observation where a cell is binucleate, e.g. have two nuclei per cell nuclei stay close together CMPO:0000213 binuclear cell phenotype binuclear cell A phenotype observation where the duration of the mitotic chromosome condensation is increased longer mitotic chromosome condensation CMPO:0000214 increased duration of mitotic chromosome condensation phenotype increased duration of mitotic chromosome condensation A phenotype observation where the duration of the mitotic chromosome condensation is decreased CMPO:0000215 decreased duration of mitotic chromosome condensation phenotype decreased duration of mitotic chromosome condensation A phenotype resulting from the absence of mitotic chromosome decondensation failure in decondensation CMPO:0000216 absence of mitotic chromosome decondensation phenotype absence of mitotic chromosome decondensation A phenotype resulting in the absence of mitotic process CMPO:0000217 absence of mitotic process phenotype absence of mitotic process A phenotype observation at the level of mitotic chromosome condensation CMPO:0000218 mitotic chromosome condensation phenotype mitotic chromosome condensation phenotype A phenotype observation at the level of mitotic chromosome decondensation CMPO:0000219 mitotic chromosome decondensation phenotype mitotic chromosome decondensation A phenotype where the apoptosis process is observed CMPO:0000220 cell apoptosis phenotype cell apoptosis phenotype increased number of apoptosis phenotypes in population CMPO:0000221 more apoptosis in population decreased number of apoptosis phenotypes in population CMPO:0000222 less apoptosis in population A phenotype observation where the thickness of the axon has increased. CMPO:0000223 increased axon thickness phenotype increased axon thickness A phenotype observation where the thickness of the axon has decreased. CMPO:0000224 decreased axon thickness phenotype decresed axon thickness A phenotype observation at the level of a axon where the components length has increased. CMPO:0000227 increased axon length phenotype increased axon length A phenotype observation at the level of a axon where the components length has decreased. CMPO:0000228 decreased axon length phenotype decreased axon length cell fusion event CMPO:0000229 plasma membrane fusion occurance phenotype plasma membrane fusion occurance A phenotype where the cell migration process occurs at an increased rate, typically observed as a faster moving cell PMID:20360735 CMPO:0000232 increased rate of cell migration process phenotype increased rate of cell migration process A phenotype where the cell migration process occurs at an redcued rate, typically observed as a slower moving cell decreased speed of cell migration CMPO:0000233 decreased rate of cell migration process phenotype decreased rate of cell migration process A phenotype observation at the level of the whole cell relating to the cell's movement CMPO:0000234 cell movement phenotype cell movement A phenotype observation at the level of the cell movement where cell movement is increased CMPO:0000235 increased cell movement phenotype increased cell movement A phenotype observation at the level of the cell movement where the cell moves faster than normal/wild type. cell moves faster increased cell migration speed CMPO:0000236 increased cell movement speed A phenotype observation at the level of the cell movement where the distance travelled by the cell is increased. The distance is measured as the euclidean distance between start and end point of the cell trajectory. cells cover a longer distance increased cell migration distance CMPO:0000237 increased cell movement distance A phenotype observation at the level of the cell movement where cell movement is decreased CMPO:0000238 decreased cell movement phenotype decreased cell movement A phenotype observation at the level of the cell movement where the distance travelled by the cell is decreased. The distance is measured as the euclidean distance between start and end point of the cell trajectory. cells cover a shorter distance CMPO:0000239 decreased cell movement distance A phenotype observation at the level of the cell movement where the cell moves slower than normal/wild type. cell moves slower CMPO:0000240 decreased cell movement speed increased number of cells in population phenotype high cell number in population increased proliferation CMPO:0000241 proliferating cells A phenotype of a cell contraction caused by an actin filament-based process in which cytoplasmic actin filaments slide past one another resulting in contraction of all or part of the cell body. cell contraction CMPO:0000243 actin-mediated cell contraction phenotype actin-mediated cell contraction A phenotype where the directed, self-propelled movement of a cellular component without the involvement of an external agent such as a transporter or a pore is observed CMPO:0000244 cell component movement phenotype cell component movement A phenotype observation of the controlled release of a substance by a cell. CMPO:0000245 cell secretion phenotype cell secretion phenotype A phenotype observation where the rate of release of proteins from a cell is increased PMID:22660414 enhanced protein secretion CMPO:0000246 increased rate of protein secretion A phenotype observation where the rate of release of proteins from a cell is decreased inhibition of protein secretion CMPO:0000247 decreased rate of protein secretion A phenotype observation at the level of the nucleus relating to the nuclear morphology CMPO:0000249 nuclear morphology phenotype nuclear morphology A phenotype observation at the level of the golgi relating to the golgi's morphology CMPO:0000250 golgi morphology phenotype golgi morphology A phenotype observation at the level of the cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. CMPO:0000251 cilium phenotype cilium phenotype A phenotype observation at the level of a cilium relating to the components shape, size or structure CMPO:0000252 cilium morphology phenotype cilium morphology A quality that inherers in a single or whole cell. CMPO:0000258 single cell phenotype single cell phenotype A quality that inheres in the cellular component of a cell CMPO:0000259 cellular component phenotype cellular component phenotype A phenotype observation at the level of the cell shape where the cell has a geometric shape with straight edges PMID:21893601 CMPO:0000261 request geometric shape in pato geometric cell phenotype geometric cell Fragmented and condensed DNA during or following apoptosis CMPO:0000262 apoptotic DNA apoptotic DNA Increased occurrence of mitotic cells increased number of mitotic cells increased occurrence of mitosis CMPO:0000263 more cells in M phase decreased occurrence of mitotic cells in population decreased number of cell in mitosis decreased number of mitotic cells decreased occurrence of mitosis less cells in M phase CMPO:0000264 fewer cells in M phase A phenotype observation at the level of the M phase of the mitotic cell cycle CMPO:0000265 M phase mitotic phenotype M phase mitotic phenotype A phenotype observation where more lamellipoda is localised to one side of the cell with respect to the other PMID:21893601 asymmetric lamellae CMPO:0000266 asymmetric lamellipodia phenotype asymmetric lamellipodia A phenotype observation at the level of the cell shape where the cell has a star-like or bristly shape PMID:21893601 spiky cell CMPO:0000267 star shaped cell phenotype star shaped cell A phenotype observation at the level of the cell shape where the cell has a star-like or bristly shape PMID:21893601 CMPO:0000268 spiny shaped cell phenotype spiny shaped cell A population of cells where the cells exhibit a high variability of size variable cell size CMPO:0000269 increased variability of cell size in population A population of cells where the cells exhibit a high variability of shape variable cell shape CMPO:0000270 increased variability of cell shape in population A phenotype observation at the level of the cortical actin cytoskeleton, the portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane. peripheral actin phenotype CMPO:0000271 cortical actin cytoskeleton phenotype cortical actin cytoskeleton phenotype A phenotype observation at the level of the cortical actin cytoskeleton where the components mass has increased. PMID:21893601 increased peripheral actin CMPO:0000272 increased cortical actin cytoskeleton mass phenotype increased cortical actin cytoskeleton mass A phenotype observation at the level of the cortical actin cytoskeleton where the components mass has decreased. PMID:21893601 decreased peripheral actin CMPO:0000273 decreased cortical actin cytoskeleton mass phenotype decreased cortical actin cytoskeleton mass A phenotype observation at the level of the cortical actin cytoskeleton where the component shows an irregular organization PMID:21893601 disorganised peripheral actin phenotype CMPO:0000274 disorganised cortical actin cytoskeleton phenotype disorganised cortical actin cytoskeleton A phenotype observation at the level of a lamellipodia where the components width has increased. PMID:21893601 increased width of lamellae CMPO:0000276 increased lamellipodia width phenotype increased lamellipodia width A phenotype observation at the level of a lamellipodia where the components width has decreased. PMID:21893601 decreased width of lamellae CMPO:0000277 decreased lamellipodia width phenotype decreased lamellipodia width A phenotype observation where the lamellipodia is shaped in the form of a fan. PMID:21893601 motile lamellae CMPO:0000278 fan-shaped lamellipodia phenotype fan-shaped lamellipodia A phenotype observation at the level of a cell with an increased amount of lamellipodia. CMPO:0000279 lamellipodium phenotype lamellipodium phenotype A phenotype observation at the level of a cellular component relating to a prolongation or process extending from a cell, e.g. a cilium, lamellipodium or axon. CMPO:0000280 cell projection phenotype cell projection phenotype A phenotype observation at the level of the filopodium; a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast. CMPO:0000281 filopodium phenotype filopodium Cells not stopping at confluence and growing on top of each other in layers PMID:21893601 layered cells CMPO:0000282 layered cells in population A phenotype observation at the level of the actin cytoskeleton, the part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. CMPO:0000283 actin cytoskeleton phenotype actin cytoskeleton A phenotype observation at the level of a actin cytoskeleton where the components mass has increased PMID:21893601 CMPO:0000284 increased actin cytoskeleton mass phenotype increased actin cytoskeleton mass A phenotype observation at the level of a actin cytoskeleton where the components mass has decreased. PMID:21893601 CMPO:0000285 decreased actin cytoskeleton mass phenotype decreased actin cytoskeleton mass A phenotype observation where microtubules form clump-like structures as opposed to filaments PMID:21893601 microtubule clumps CMPO:0000286 aggregated microtubules phenotype aggregated microtubules A phenotype observation where the microtubules form two crescent shaped brackets around the nucleus PMID:21893601 CMPO:0000287 microtubules nuclear bracket phenotype microtubules nuclear bracket A phenotype observation where the microtubules form a ring around the nucleus PMID:21893601 microtubule nuclear ring CMPO:0000288 microtubules nuclear ring phenotype microtubules nuclear ring A phenotype observation at the level of any stress fibers where the components number has increased. pmid:21893601 more actin stress fibers CMPO:0000289 increased amount of stress fibers phenotype increased amount of stress fibers A phenotype observation where actin is observed as small patches or spots all over the cell puncta actin filament phenotype CMPO:0000290 punctate actin foci phenotype punctate actin foci A phenotype observation where a cell has an increased amount of actin observed as small patches or spots all over the cell PMID:21893601 increased actin puncta more actin puncta CMPO:0000291 increased amount of punctate actin foci phenotype increased amount of punctate actin foci A phenotype of a culture in which cells grow as a monolayer that is attached to the culture substrate. http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20216 CMPO:0000292 cell population layer phenotype cell layer phenotype Loss of sheet like monolayer leading to empty patches lost cell monolayer CMPO:0000293 loss of cell monolayer loss of cell monolayer A phenotype observation where many actin filaments are observed in or around the nucleus PMID: 21893601 increased nuclear actin CMPO:0000294 increased actin localised to the nucleus A phenotype observation where many actin filaments are observed in the cytoplasm PMID: 21893601 increased cytoplasmic actin CMPO:0000296 increased actin localised to the cytoplasm A phenotype observation at the level of stress fibers localized to the cell cortex where the components number has increased. pmid:21893601 more cortical actin stress fibers CMPO:0000297 Increased amount of actin stress fibers in the cortical area increased amount of stress fibers located in the cell cortex phenotype increased amount of stress fibers located in the cell cortex A phenotype observation at the level of stress fibers where the components number has increased and formed transverse arcs which are located in the cell cortex pmid:21893601 more transverse actin stress fibers CMPO:0000298 Increased amount of actin stress fibers, forming transverse arcs located in the cell cortex increased amount of transverse stress fibers A phenotype observation at the level of stress fibers where the components number has increased and formed a zig zag pattern across the cell pmid:21893601 more zig-zag actin stress fibers CMPO:0000299 Increased amount of actin stress fibers, with zig-zag pattern across the cell increased amount of zig-zag stress fibers Increased cells that are multinucleated CMPO:0000300 more multinucleate cells Absence of cells PMID:21893601 CMPO:0000301 no cells phenotype no cells A phenotype observation where the microtubules form a ring around the nucleus PMID:21893601 nuclear actin ring CMPO:0000302 actin nuclear ring phenotype actin nuclear ring A phenotype observation at the level of a cellular component relating to the components shape, size or structure CMPO:0000303 cell component morphology phenotype cell component morphology A phenotype of a cell where a particular process is arrested, or ends earlier in time than expected CMPO:0000304 cell cycle arrested phenotype cell cycle arrested A phenotype of a cell arrested in mitotic metaphase PMID:20360735 metaphase arrest CMPO:0000305 metaphase arrested phenotype metaphase arrested A phenotype of a cell where a particular process is delayed CMPO:0000306 delayed process phenotype delayed process A phenotype of a cell where mitotic metaphase is delayed PMID:20360735 metaphase delay CMPO:0000307 metaphase delayed phenotype metaphase delayed A phenotype where the cell migration is impaired abnormal cell migration CMPO:0000309 impaired cell migration A phenotype where the cell migration process occurs for longer, typically observed as a cell moving a further distance PMID:20360735 CMPO:0000312 increased duration of cell migration process phenotype increased duration of cell migration process A phenotype where the cell migration process duration is reduced, typically observed as a cell moving a shorter distance CMPO:0000313 decreased duration of cell migration process phenotype decreased duration of cell migration process A phenotype observation at the level of the exit from mitosis CMPO:0000314 exit from mitosis phenotype exit from mitosis A phenotype observation at the level of a cellular process where the cell process is absent cell physiology phenotype CMPO:0000315 absence of cell process phenotype absence of cell process A phenotype observation of the process in which the cell growth is abnormal CMPO:0000316 abnormal cell growth phenotype abnormal cell growth A phenotype observation of the process in which the cell growth is arrested CMPO:0000317 cell growth arrested phenotype cell growth arrested A phenotype observation where the rate of release of proteins from a cell is mildly decreased PMID:22660414 mild inhibition of protein secretion CMPO:0000318 mild decrease in rate of protein secretion A phenotype observation where the rate of release of proteins from a cell is severly decreased PMID:22660414 strong inhibition of protein secretion CMPO:0000319 strong decrease in rate of protein secretion A phenotype observation where there is an increased occurance of cell spreading CMPO:0000320 increased cell spreading phenotype increased cell spreading A phenotype observation where there is a mild increase of cell spreading PMID:19667130 moderate cell spreading CMPO:0000321 mild increase of cell spreading phenotype mild increase of cell spreading A phenotype observation where there is a severe increase in cell spreading extensive cell spreading CMPO:0000322 strong increase of cell spreading phenotype strong increase of cell spreading A phenotype observation where there is a decreased occurance of cell spreading PMID:19667130 poor cell spreading CMPO:0000323 decreased cell spreading phenotype decreased cell spreading A phenotype observation where cell spreading is absent no spreading cells CMPO:0000324 absence of cell spreading phenotype absence of cell spreading A phenotype observation where a cell shows a thin and large projected areas, with developed matrix adhesions at the cell periphery, as opposed to round cells with no or few adhesion sites spreading cell shape CMPO:0000325 spread cell morphology phenotype spread cell morphology A phenotype observation of the process in which the chromosome segregation is abnormal PMID:20360735 chromatin bridges lagging chromosomes multiple DNA masses segregation problems CMPO:0000326 abnormal chromosome segregation phenotype abnormal chromosome segregation A phenotype observation at the level of the mitotic prophase of the cell cycle CMPO:0000327 mitotic prophase phenotype mitotic prophase phenotype A phenotype observation where the duration of the mitotic prophase of the cell cycle is increased CMPO:0000328 increased duration of mitotic prophase phenotype increased duration of mitotic prophase A phenotype observation where the duration of the mitotic prophase of the cell cycle is decreased CMPO:0000329 decreased duration of mitotic prophase phenotype decreased duration of mitotic prophase A phenotype observation where the frequency of a process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB is decreased. decreased number of oscillations; the amplitude of the first peak is comparable to control, although the duration may be increased; the time of the second and third peaks is delayed, due to greater interval times between termination and initiation of nuclear translocation responses PMID:23300644 decreased NF-kB oscillation CMPO:0000330 decreased frequency of negative regulation of NF-kappaB transcription factor activity phenotype decreased frequency of negative regulation of NF-kappaB transcription factor activity A phenotype observation where the frequency of a process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB is increased. increased number of oscillations; the amplitude of the second and third peak is increased and nuclear translocation responses occur at increased intervals. PMID:23300644 increased NF-kB oscillation CMPO:0000331 increased frequency of negative regulation of NF-kappaB transcription factor activity phenotype increased frequency of negative regulation of NF-kappaB transcription factor activity A phenotype observation where the frequency of a process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB is increased. increased number of oscillations; the amplitude of the second and third peak is increased and nuclear translocation responses occur at increased intervals. PMID:23300644 no NF-kB oscillation phenotype CMPO:0000332 cytoplasmic sequestering of NF-kappaB phenotype cytoplasmic sequestering of NF-kappaB A phenotype observation where the release of NF-kappaB from specific molecules in the cytoplasm to which it was bound, thereby allowing its translocation into the nucleus, is abnormal. contains all cases that are significantly different from the rest, but don't share any clear commonalities. NF-kB oscillation patterns are not synchronized within a cell population, oscillation amplitude and frequency follow erratic patterns PMID:23300644 different NF-kB oscillation phenotype CMPO:0000333 abnormal release of cytoplasmic sequestered NF-kappaB phenotype abnormal release of cytoplasmic sequestered NF-kappaB A phenotype observation where any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. CMPO:0000334 regulation of process phenotype regulation of process phenotype A phenotype obervation where the nuclear body's color brightness is relatively high. pmid:22884692 increased intensity of nuclear body CMPO:0000335 bright nuclear body phenotype bright nuclear body A phenotype observation where the shape of the focal adhesion has every part of the surface or the circumference equidistant from the center. CMPO:0000337 round focal adhesion A phenotype of a cell that is arrested at mitosis PMID:20360735 mitotic arrest CMPO:0000338 mitosis arrested A population of cells where there is an increased number of large cells in the population large cells CMPO:0000340 increased cell size in population increased cell size in population A phenotype observation at the level of the nucleus underoging Pyknosis, or karyopyknosis, consisting of the irreversible condensation of chromatin in the nucleus of a cell undergoing necrosis or apoptosis. pyknotic cell pyknotic nucleus CMPO:0000341 pyknotic nuclear phenotype A phenotype of a cell arrested in mitotic prometaphase prometaphase arrest CMPO:0000343 prometaphase arrested phenotype prometaphase arrested A phenotype of a cell where mitotic prometaphase is delayed prometaphase delay CMPO:0000344 prometaphase delayed phenotype prometaphase delayed A population of cells where the nuclei exhibit a high variability of shape variable cell shape CMPO:0000345 increased variability of nuclear shape in population A phenotype observation where the rate of intracellular protein transport is decreased pmid:21795383 CMPO:0000346 decreased rate of intracellular protein transport phenotype decreased rate of intracellular protein transport A phenotype resulting in the absence of mitotic metaphase process CMPO:0000347 absence of mitotic metaphase process phenotype absence of mitotic metaphase A phenotype observation at the level of the cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis. metaphase alignment problem CMPO:0000348 mitotic metaphase plate congression phenotype mitotic metaphase plate congression A phenotype where an increased formation of a cell surface protrusion, such as a lamellipodium or filopodium, at the leading edge of a migrating cell is observed. increased protrusive activity CMPO:0000349 increased substrate-dependent cell migration, cell extension phenotype increased substrate-dependent cell migration, cell extension A phenotype where an increased occurrence of the orderly movement of a cell from one site to another along a substrate such as the extracellular matrix is observed. increased directional cell migration CMPO:0000350 increased substrate-dependent cell migration phenotype increased substrate-dependent cell migration A phenotype where an increased occurance of any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins, is observed. microtubule processes CMPO:0000351 increased microtubule-based processes phenotype increased microtubule-based processes A phenotype observation of the process in which a cell increases in size due to polarized growth from one end of a cell. increased polar cell elongation CMPO:0000353 increased monopolar cell elongation phenotype increased monopolar cell elongation A phenotype observation of the process in which a cell decreases in size due to polarized growth from one end of a cell. decreased polar cell elongation CMPO:0000354 decreased monopolar cell elongation phenotype decreased monopolar cell elongation A phenotype of a cell contraction caused by an actin filament-based process in which cytoplasmic actin filaments slide past one another resulting in mild contraction of all or part of the cell body. CMPO:0000355 mild actin-mediated cell contraction phenotype mild actin-mediated cell contraction A phenotype where any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in a specific location is observed cell component localization CMPO:0000356 cell component localization phenotype cell component localisation A phenotype observation where the shape of the nucleus resembles a many-lobed berry, such as a raspberry. acinus nuclear phenotype CMPO:0000357 polylobed nuclear phenotype A phenotype of a cell where the rate of DNA amplification is increased CMPO:0000358 increased rate of DNA amplification increased rate of DNA amplification A phenotype observation where a cell has an increased amount of DNA CMPO:0000359 increased amount of DNA increased amount of DNA A phenotype of a cell in which the biological process resulting in a doubling of the number of centrioles in the cell is affected pmid:18620859 centriole duplication phenotype CMPO:0000360 centriole replication phenotype centriole replication A phenotype of a cell in which the biological process resulting in a the number of centrioles is increased centriole amplification phenotype CMPO:0000361 increased centriole replication phenotype increased centriole replication A phenotype of a cell in which the biological process resulting in a the number of centrioles is decreased centriole underduplication phenotype CMPO:0000362 decreased centriole replication phenotype decreased centriole replication CMPO:0000363 protein localization to cellular component phenotype A phenotype observation at the level of the cell shape where the cell is in a shape that consists of two curves in opposite directions. PMID: 25373780 FYPO:0002760 kinked cell kinky cell sigmoid cell z-shaped cell CMPO:0000364 s-shaped cell phenotype S-shaped cell A phenotype observation at the level of the cell shape where the cell is curved along the long axis. PMID: 25373780 FYPO:0002112 CMPO:0000365 curved cell phenotype Curved cell A phenotype observation at the level of the cell shape where the shape is in the form of a pear. One end is rounded, while the other is rod-shaped. PMID: 25373780 FYPO:0002903 skittle-shaped cell CMPO:0000366 pear-shaped cell phenotype Pear-shaped cell A phenotype observation at the level of the cell shape where the shape is stubby. The cell diameter is larger than normal and the cell length is shorter than normal. PMID: 25373780 wide cell FYPO:0002106 CMPO:0000367 stubby cell phenotype Stubby cell A phenotype observation at the level of the microtubule cytoskeleton relating to the components shape, size or structure CMPO:0000368 microtubule cytoskeleton morphology phenotype microtubule cytoskeleton morphology A physical cellular phenotype in interphase of the mitotic cell cycle where the the size, shape, or structure of the microtubule cytoskeleton is observed. PMID: 25373780 FYPO:0003625 CMPO:0000369 microtubule cytoskeleton morphology during mitotic interphase microtubule cytoskeleton morphology during mitotic interphase A physical cellular phenotype which cells form cytoplasmic microtubules that are longer than normal. PMID: 25373780 FYPO:0000233 elongated cytoplasmic microtubules long cytoplasmic microtubules CMPO:0000370 elongated cytoplasmic microtubules phenotype elongated cytoplasmic microtubules A physical cellular phenotype which cells form cytoplasmic microtubules that are shorter than normal. PMID: 25373780 FYPO:0002401 shortened cytoplasmic microtubules CMPO:0000371 shortened cytoplasmic microtubules phenotype elongated cytoplasmic microtubules A phenotype observation at the level of microtubule bundle where the components number has increased. PMID: 25373780 FYPO:0003595 extra microtubule bundles increased level of MT bundles increased microtubule bundling more microtubule bundles CMPO:0000372 increased number of microtubule bundle phenotype increased number of microtubule bundle A phenotype observation at the level of the microtubule relating to the components shape, size or structure PMID: 25373780 CMPO:0000373 microtubule morphology phenotype microtubule morphology A phenotype observation at the level of the microtubule relating to the components shape, size or structure observed in mitotic interphase. PMID: 25373780 CMPO:0000374 microtubule morphology during interphase phenotype microtubule morphology during interphase An increased number of interphase microtubule phenotype in population. PMID: 25373780 CMPO:0000375 more cells with interphase microtubule phenotype more cells with interphase microtubule A phenotype observation at the level of the microtubule spindle relating to the components shape, size or structure PMID: 25373780 CMPO:0000376 microtubule spindle morphology phenotype microtubule spindle morphology A phenotype observation at the level of the microtubule spindle relating to the components shape, size or structure observed during metaphase. PMID: 25373780 CMPO:0000377 microtubule spindle morphology during metaphase phenotype microtubule spindle morphology during metaphase An increased number of metaphase microtubule spindles in population. PMID: 25373780 SP increased CMPO:0000378 more cells with metaphase microtubule spindles phenotype more cells with metaphase microtubule spindles A phenotype observation at the level of the microtubule where the microtuble are narrow, with the two opposite margins parallel. PMID: 25373780 CMPO:0000379 linear microtubule morphology phenotype linear microtubule morphology A phenotype obesrvation relating to the orgnaistation of cellular componets in the cell. CMPO:0000380 cell component organisation phenotype cell component organisation A phenotype observation relating to the organisation of cellular components in the cell. CMPO:0000381 microtubule organisation phenotype cell component organisation A phenotype observation relating to the organisation of microtubules in the cell, where the microtubules are organized into an array. PMID: 25373780 CMPO:0000382 microtubule array phenotype microtubule array An increased number of interphase microtubule array phenotype in population. PMID: 25373780 IP increased CMPO:0000383 more cells with interphase microtubule arrays phenotype more cells with interphase microtubule arrays A phenotype observation at the level of interphase of the cell cycle CMPO:0000384 interphase phenotype interphase phenotype A phenotype observation at the level of interphase of the cell cycle CMPO:0000385 mitotic interphase phenotype mitotic interphase phenotype A phenotype observation at the level of anaphase of the cell cycle CMPO:0000386 anaphase phenotype anaphase phenotype A decreased number of metaphase microtubule spindles in population. PMID: 25373780 SP reduced CMPO:0000387 fewer cells with metaphase microtubule spindles phenotype fewer cells with metaphase microtubule spindles A decreased number of interphase microtubule array phenotypes in population. PMID: 25373780 IP reduced CMPO:0000388 fewer cells with interphase microtubule arrays phenotype fewer cells with interphase microtubule arrays A phenotype observation in which a protein is observed to be localized within the Golgi apparatus. PMID: 23509072 protein localised in Golgi protein localised in Golgi apparatus protein localized to Golgi protein localized to Golgi apparatus CMPO:0000390 protein localized in golgi phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the Golgi apparatus. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23509072 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in Golgi http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in Golgi apparatus http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to Golgi http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to Golgi apparatus http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a cellular bud neck. PMID: 23509072 protein localised in bud neck protein localized in cellular bud neck protein localized to bud neck CMPO:0000391 protein localized in bud neck phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a cellular bud neck. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23509072 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in bud neck http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized in cellular bud neck http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to bud neck http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the cell periphery. PMID: 23509072 protein localised in cell periphery protein localized to cell periphery CMPO:0000392 protein localized in cell periphery phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the cell periphery. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23509072 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in cell periphery http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to cell periphery http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the cytosol. PMID: 23509072 protein localised in cytosol protein localized to cytosol CMPO:0000393 protein localized in cytosol phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the cytosol. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23509072 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in cytosol http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to cytosol http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the endoplasmic reticulum. PMID: 23509072 protein localised in endoplasmic reticulum protein localized to endoplasmic reticulum CMPO:0000394 protein localized in endoplasmic reticulum phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the endoplasmic reticulum. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23509072 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in endoplasmic reticulum http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to endoplasmic reticulum http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a mitochondrion. PMID: 23509072 protein localised in mitochondria protein localised in mitochondrion protein localized to mitochonria protein localized to mitochonrion CMPO:0000395 protein localized in mitochondrion phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a mitochondrion. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23509072 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in mitochondria http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in mitochondrion http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to mitochonria http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to mitochonrion http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the nuclear periphery. PMID: 23509072 protein localised in nuclear periphery protein localized to nuclear periphery CMPO:0000396 protein localized in nuclear periphery phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the nuclear periphery. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23509072 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in nuclear periphery http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to nuclear periphery http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the nucleolus. PMID: 23509072 protein localised in nucleolus protein localized to nucleolus CMPO:0000397 protein localized in nucleolus phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the nucleolus. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23509072 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in nucleolus http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to nucleolus http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the nucleus. PMID: 23509072 protein localised in nucleus protein localized to nucleus CMPO:0000398 protein localized in nucleus phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the nucleus. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23509072 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in nucleus http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to nucleus http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a peroxisome. PMID: 23509072 protein localised in peroxisome protein localized to peroxisome CMPO:0000399 protein localized in peroxisome phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a peroxisome. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23509072 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in peroxisome http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to peroxisome http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within punctate foci PMID: 23509072 protein localised in punctate foci protein localized to punctate foci CMPO:0000400 protein localized in punctate foci phenotype A phenotype observation in which a protein is observed to be localized within punctate foci http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23509072 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in punctate foci http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to punctate foci http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a vacuole. PMID: 23509072 protein localised in vacuole protein localized to vacuole CMPO:0000401 protein localized in vacuole phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a vacuole. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23509072 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in vacuole http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to vacuole http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a vacuolar membrane. PMID: 23509072 protein localised in vacuolar membrane protein localized to vacuolar membrane CMPO:0000402 protein localized in vacuolar membrane phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a vacuolar membrane. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23509072 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in vacuolar membrane http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to vacuolar membrane http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the nuclear body. protein localised in nuclear body protein localized to nuclear body CMPO:0000403 protein localized to nuclear body http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the nuclear body. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in nuclear body http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized to nuclear body http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a Cajal body. PubMed ID:24127217 protein localised in Cajal body phenotype CMPO:0000404 protein localized in Cajal body phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a Cajal body. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed ID:24127217 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in Cajal body phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a nuclear speckle. PubMed ID:24127217 protein localised in nuclear speckle phenotype CMPO:0000405 protein localized in nuclear speckle phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a nuclear speckle. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed ID:24127217 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in nuclear speckle phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a paraspeckle. PubMed ID:24127217 protein localised in paraspeckle phenotype CMPO:0000406 protein localized in paraspeckle phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a paraspeckle. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed ID:24127217 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in paraspeckle phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a PML body. PubMed ID:24127217 protein localised in PML body phenotype protein localised in Promyelocytic Leukemia nuclear body phenotype protein localized in Promyelocytic Leukemia nuclear body phenotype CMPO:0000407 protein localized in PML body phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a PML body. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed ID:24127217 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in PML body phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in Promyelocytic Leukemia nuclear body phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized in Promyelocytic Leukemia nuclear body phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a polycomb body. PubMed ID:24127217 protein localised in PcG body phenotype protein localized in PcG body phenotype protein localized in polycomb body phenotype CMPO:0000408 protein localized in polycomb body phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a polycomb body. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed ID:24127217 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in PcG body phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized in PcG body phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localized in polycomb body phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a Sam68 nuclear body. PubMed ID:24127217 protein localised in Sam68 nuclear body phenotype CMPO:0000409 protein localized in Sam68 nuclear body phenotype A phenotype observation in which a protein is observed to be localized within a Sam68 nuclear body. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed ID:24127217 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in Sam68 nuclear body phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A decreased number of post-anaphase or G1 phase microtubule arrays in population phenotype PMID: 25373780 PAA decreased fewer cells with post-anaphase microtubule arrays CMPO:0000410 fewer cells with G1 phase microtubule arrays phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A decreased number of post-anaphase or G1 phase microtubule arrays in population phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 25373780 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PAA decreased http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern fewer cells with post-anaphase microtubule arrays http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A decreased number of post-mitotic interphase or S phase microtubule arrays in population phenotype PMID: 25373780 IP2 decreased fewer cells with post-mitotic interphase microtubule arrays CMPO:0000411 fewer cells with S phase microtubule arrays phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A decreased number of post-mitotic interphase or S phase microtubule arrays in population phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 25373780 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern IP2 decreased http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern fewer cells with post-mitotic interphase microtubule arrays http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern An increased number of post-anaphase or G1 phase microtubule arrays in population phenotype PMID: 25373780 PAA increased more cells with post-anaphase microtubule arrays CMPO:0000412 more cells with G1 phase microtubule arrays phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern An increased number of post-anaphase or G1 phase microtubule arrays in population phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 25373780 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PAA increased http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern more cells with post-anaphase microtubule arrays http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern An increased number of post-mitotic interphase or S phase microtubule arrays in population phenotype PMID: 25373780 IP2 increased more cells with post-mitotic interphase microtubule arrays CMPO:0000413 more cells with S phase microtubule arrays phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern An increased number of post-mitotic interphase or S phase microtubule arrays in population phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 25373780 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern IP2 increased http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern more cells with post-mitotic interphase microtubule arrays http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation of respone to stress process within a cell. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). CMPO:0000414 cell response to stress phenotype cell response to stress A phenotype observation of a process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. DNA damage CMPO:0000415 cell response to DNA damage phenotype cell response to DNA damage The population has a decreased number of cells forming cell-cell aggregates. PMID:24446484 defective cell-cell aggregation CMPO:0000416 fewer aggregated cells in population phenotype fewer aggregated cells in population A phenotype observation in which a protein is absent or decreased from the expected localisation of protein localisation process PMID: 23547032 protein absent from localisation to cellular component CMPO:0000417 example 'the smt3allR mutant does not show localization at the bud neck' lack of protein in cell component localization phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is absent or decreased from the expected localisation of protein localisation process http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID: 23547032 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein absent from localisation to cellular component http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation at the level of a response to stimulus process CMPO:0000419 response to stimulus phenotype A phenotype observation at the level of a response to stimulus process CMPO:0000420 response to chemical phenotype A phenotype observation at the level of a response to stimulus process CMPO:0000421 cellular response to chemical stimulus phenotype A phenotype observation at the level of telophase of the cell cycle CMPO:0000422 telophase phenotype telophase phenotype A phenotype observation at the level of mitotic telophase of the cell cycle CMPO:0000423 mitotic telophase phenotype telophase phenotype A phenotype of a cell where the mitotic telophase process is arrested, or ends earlier in time than expected CMPO:0000424 telophase arrested phenotype telophase arrested A phenotype observation in which a protein is observed to be localized within a centrosome. PMID:23086237 protein localisation in centrosome protein localised in centrosome protein localised to centrosome protein localization in centrosome CMPO:0000425 protein localized in centrosome phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a centrosome. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID:23086237 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localisation in centrosome http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in centrosome http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised to centrosome http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localization in centrosome http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a nuclear pore. PMID:23845946 protein localisation in nuclear pore protein localised in nuclear pore protein localised to nuclear pore protein localization in nuclear pore CMPO:0000426 protein localized in nuclear pore phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a nuclear pore. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PMID:23845946 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localisation in nuclear pore http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in nuclear pore http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised to nuclear pore http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localization in nuclear pore http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A collection of qualities that inhere in any constituent part of the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules. CMPO:0000427 kinetochore phenotype kinetochore phenotype A phenotype observation at the level of the cell shape where the cell is fan-shaped CMPO:0000428 fan-shaped cell phenotype fan-shaped cell A phenotype observation at the level of the cell protein cell protein phenotype CMPO:0000429 cell polypeptide phenotype cell protein phenotype A cell phenotype in which the amount of a specific substance measured in a cell differs from normal. FYPO:0000989 PomBase:mah CMPO:0000430 altered level of substance in cell altered level of substance in cell A cell phenotype in which the amount of polypetide measured in a cell differs from normal. CMPO:0000431 altered level of polypetide in cell altered level of polypeptide in cell A cell phenotype in which the amount of polypetide measured in a cell nucleus differs from normal. altered level of protein in cell nucleus CMPO:0000432 altered level of polypetide in cell nucleus altered level of substance in cell nucleus A cell phenotype in which the amount of polypetide measured in a cell nucleus increases from normal. increased level of protein in cell nucleus CMPO:0000433 increased level of polypetide in cell nucleus incressed level of polypetide in cell nucleus A cell phenotype in which the amount of polypetide measured in a cell nucleus descreases from normal. decreased level of protein in cell nucleus CMPO:0000434 decreased level of polypetide in cell nucleus descreased level of polypetide in cell nucleus A phenotype observation where any process that stops, prevents, or reduces the frequency, rate or extent of the movement of proteins from the cytoplasm into the nucleus. CMPO:0000435 negative regulation of protein import into nucleus phenotype regulation of process phenotype A phenotype observation where any process that starts or increases the frequency, rate or extent of the movement of proteins from the cytoplasm into the nucleus. CMPO:0000436 positive regulation of protein import into nucleus phenotype positive regulation of protein import into nucleus A phenotype where the mitotic cell cycle phase is abnormal CMPO:0000437 abnormal mitotic cell cycle phase phenotype abnormal mitotic cell cycle phase A physical cellular phenotype in interphase of the mitotic cell cycle where the the size, shape, or structure of the microtubule cytoskeleton is abnormal. PMID: 25373780 FYPO:0003625 CMPO:0000438 abnormal microtubule cytoskeleton morphology during mitotic interphase abnormal microtubule cytoskeleton morphology during mitotic interphase A phenotype observation in which a protein is not localized within a cellular bud neck. CMPO:0000439 absence of protein localized in bud neck phenotype A phenotype observation in which a protein is not localized within a cellular bud neck. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within an actin filament. PubMed: 22361696 protein localised in actin filament phenotype CMPO:0000440 protein localized in actin filament phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within an actin filament. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed: 22361696 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in actin filament phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within an intermediate filament. PubMed: 22361696 protein localised in intermediate filament phenotype CMPO:0000441 protein localized in intermediate filament phenotype A phenotype observation in which a protein is observed to be localized within an intermediate filament. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed: 22361696 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in intermediate filament phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a microtubule. PubMed: 22361696 protein localised in microtubule phenotype CMPO:0000442 protein localized in microtubule phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a microtubule. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed: 22361696 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in microtubule phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized the nuclear membrane. PubMed: 22361696 protein localised in nuclear envelope phenotype protein localised in nuclear membrane phenotype CMPO:0000443 protein localized in nuclear membrane phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized the nuclear membrane. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed: 22361696 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in nuclear membrane phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the nucleolar fibrillar center. PubMed: 22361696 protein localised in nucleoli fibrillar center phenotype CMPO:0000444 protein localized in nucleoli fibrillar center phenotype A phenotype observation in which a protein is observed to be localized within the nucleolar fibrillar center. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed: 22361696 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in nucleoli fibrillar center phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the nucloplasm. PubMed: 22361696 protein localised in nucleoplasm phenotype CMPO:0000445 protein localized in nucleoplasm phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the nucloplasm. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed: 22361696 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in nucleoplasm phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the plasma membrane. PubMed: 22361696 protein localised in plasma membrane phenotype CMPO:0000446 protein localized in plasma membrane phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within the plasma membrane. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed: 22361696 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in plasma membrane phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype observation in which a protein is observed to be localized within a vesicle. PubMed: 22361696 protein localised in vesicle phenotype CMPO:0000447 protein localized in vesicle phenotype A phenotype observation in which a protein is observed to be localized within a vesicle. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PubMed: 22361696 http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern protein localised in vesicle phenotype http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A phenotype where the the cells are killing either its own cells or those of another organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. CMPO:0000448 cell killing phenotype cell killing phenotype A phenotype where the the cells are killing either its own cells or those of another organism. The directed killing of a tumor cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. 'T cell mediated cytotoxicity directed against tumor cell target phenotype CMPO:0000449 T cell mediated killing against a tumor cell phenotype T cell mediated killing against a tumor cell phenotype The population has an increased number of cells forming cell-cell aggregates. CMPO:0000450 more aggregated cells in population phenotype more aggregated cells in population phenotype A phenotype observation where the area of the nucelus has increased. CMPO:0000451 increased nuclear area phenotype increased nuclear area phenotype A phenotype observation where the area of the nucelus has decreased. CMPO:0000452 decreased nuclear area phenotype decreased nuclear area phenotype A population of cells where there is an increased number of small cells in the population small cells CMPO:0000453 decreased cell size in population decreased cell size in population A phenotype observation where a cellular componet is localised to one side of the cell with respect to the other asymmetric component CMPO:0000454 asymmetric cellular component phenotype asymmetric component A cell phenotype in which the amount of polypetide measured in a cell is decreased from normal. decreased level of protein in the cell CMPO:0000455 decreased level of polypetide in the cell decreased level of polypetide in the cell A cell phenotype in which the amount of polypetide measured in a cell is increased from normal. increased level of protein in the cell CMPO:0000456 increased level of polypetide in the cell increased level of polypetide in the cell A population of cells where there is is an increased number of cells with a decreased nucleus to cell area ratio CMPO:0000457 decreased nucleus to cell area ratio decreased nucleus to cell area ratio A population of cells where there is is an increased number of cells with an increased nucleus to cell area ratio CMPO:0000458 increased nucleus to cell area ratio increased nucleus to cell area ratio inheres in at all times has phenotype