]> 0.5 Gene Regulation Ontology (GRO) Vivian Lee April 20, 2010 Elena Beisswanger The Gene Regulation Ontology (GRO) covers gene regulatory processes occurring on the intracellular level and molecular entities participating in these processes. Jung-jae Kim Andrea Splendiani GRO definition explaining the meaning of a class or property. If the definition was taken from an external resource a reference is given in brackets. negative positive positive and negative unknown Reference to a similar term in an external database or terminological resource. An exact synonyms of the given ontology term. AP2-EREBP-related domain A domain consisting of the AP2 (APETALA2) and EREBPs (ethylene-responsive element binding proteins) related DNA-binding sequence. AP2-EREBP related transcription factor A transcription factor containing the AP2 (APETALA2) and EREBPs (ethylene-responsive element binding proteins) related DNA-binding domain, which plays a variety of roles throughout the plant life cycle. acetylation A reaction that introduces an acetyl functional group into an organic compound. [http://en.wikipedia.org/wiki/Acetylation] activation positive Any process that activates, maintains or increases the frequency, rate or extent of an action. activation of polymerase Any process that initiates the activity of the inactive enzyme polymerase. activation of process Any process that activates or increases the frequency, rate or extent of a process. activation of protein Any process that initiates the activity of the inactive form of a protein. activation of transcription regulator activity Any process that activates or increases the frequency, rate or extent of activity of a transcription regulator, any factor plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor (modified from [GO:0051091, GO:0030528]) affecting agonist Any molecule that improves the activity of a different molecule; e.g., a hormone, which acts as an agonist when it binds to its receptor, thus triggering a biochemical response. [http://www.combichemistry.com/medical-chemistry-glossary.html] amino acid CHEBI:33709 amino acids Carboxylic acids containing one or more amino groups. [CHEBI:33709] IMR:0001695 amino acid antagonist An agent that opposes the action or reduces the physiological activity of another. antisense RNA SO:0000644 antisense_RNA Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA. [SO:0000644] apoenzyme a protein that combines with a coenzyme to form an active enzyme [http://wordnet.princeton.edu/perl/webwn?s=apoenzyme] archaebacterium Ancient life forms that evolved separately from bacteria and blue-green algae. [http://wordnet.princeton.edu/perl/webwn?s=archaebacterium] NCBI Taxonomy ID: 2157 Archaea architectural proteins Proteins that bend DNA. atom The smallest part of an element that still has all properties of that element. Its nucleus consists of protons and neutrons and is surrounded by orbiting electrons. [http://www.nsc.org/EHC/guidebks/wippglos.htm] attenuator A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. [SO:0000140] SO:0000140 attenuator bacterial RNA polymerase promoter A DNA sequence to which bacterial RNA polymerase binds, to begin transcription. [SO:0000613] SO:0000613 bacterial RNApol promoter bacteriophage A virus that infects bacteria. Also called a phage. [www.accessexcellence.org/RC/AB/WYW/wkbooks/SFTS/glossary.html] NCBI Taxonomy ID: 38018 unidentified phage bacterium Any of the unicellular prokaryotic organisms, which vary in terms of morphology, oxygen and nutritional requirements and motility and can exist either as independent (free-living) organisms or as parasites (dependent upon another organism for life). NCBI Taxonomy ID: 2 Bacteria basic domain A domain containing a basic region that mediates sequence-specific DNA-binding. basic domain transcription factor A transcription factor containing basic domain. behavior GO:0007610 behavior The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. [GO:0007610] beta barrel alpha helix domain A DNA binding domain usual found in the viral protein E2, in which it forms a dimeric beta barrel, with each subunit contributing an anti-parallel 4-stranded beta sheet half-barrel. The topology of each subunit is beta1-1-beta2-beta3-2-beta4. Helix 1 is the recognition helix housing all of the amino acid residues involved in direct DNA sequence specification. Upon dimerisation, strands beta2 and beta4 at the edges of each subunit participate in a continuous hydrogen-bonding network, which results in an 8-stranded beta-barrel. The dimer interface is extensive, made up of hydrogen bonds between subunits and a substantial hydrophobic beta-barrel core. (modified from [InterPro:IPR000427] beta-barrel alpha-helix domain transcription factor A transcription factor containing beta-barrel alpha-helix domain. beta scaffold domain transcription factor with minor groove contacts A transcription factor containing beta scaffold domain with minor groove contacts beta scaffold domain with minor groove contacts A domain containing beta scaffold structure and usually binding to the DNA minor groove. bidirectional promoter Promoter sequences between divergently transcribed neighbouring gene pairs that initiate transcription in both directions. [http://www.everythingbio.com/glos/definition.php?word=bidirectional+promoters] binding GO:0005488 binding The selective, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. [GO:0005488] binding assay An analytic procedure in which binding is studied involves the labelling of an expressed protein. binding of DNA binding domain of protein to DNA Selective interaction of a DNA binding domain of a protein with DNA. binding of molecular entity Selective interaction of a molecule entity with other substance. binding of protein Selective interaction of a protein with other molecules. binding of protein to DNA The selective interaction of a protein or protein complex with a deoxyribonucleotide, any compound consisting of a deoxyribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety. binding of protein to protein binding site of DNA Selective interaction of a protein with a specific site on DNA which forms a chemical bond. binding of protein to protein binding site of protein Selective interaction of a protein with a specific site on other proteins which forms a chemical bond. binding of RNA polymerase to DNA Selective interaction of RNA polymerase with DNA binding of TF to TF binding site of DNA Selective interaction of a transcription factor with a specific site on DNA which forms a chemical bond. binding of TF to TF binding site of protein Selective interaction of a transcription factor with one or more specific sites on a protein. binding of transcription activator to enhancer The selective interaction of a transcription activator with a cis-acting sequence that increases the utilization of (some) eukaryotic promoter. binding of transcription factor to DNA The function of binding to a specific DNA sequence in order to modulate transcription. [GO:0003700] binding of transcription factor to operator Selective interaction of a transcription factor with an operator binding of transcription repressor to silencer Selective interaction of a transcription repressor with a collection of short DNA sequence elements which suppress the transcription of an adjacent gene or genes. binding of translation initiation complex to RNA RNA binding of translation initiation complex Selective interaction of translation initiation complex with RNA which leaves the functional ribosome at the AUG, with the methionyl/formyl-methionyl-tRNA positioned at the P site. binding site of protein A region on a protein that forms a chemical bond with other molecules. binding to binding site of protein Selective interaction of a molecule with a specific site on a protein which forms a chemical bond. binding to micro RNA Interacting selectively with microRNA. miRNA binding microRNA binding binding to molecular entity Interacting selectively with a molecular entity. molecular binding binding to protein GO:0005515 protein binding Interacting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).[GO:0005515] binding to RNA GO:0003723 RNA binding Interacting selectively with an RNA molecule or a portion thereof. [GO:0003723] RNA binding biofilm A slime layer that develops naturally when bacteria congregate on surfaces. [publications.nigms.nih.gov/thenewgenetics/glossary.htm] biomass Total mass of all the organisms of a given type and/or in a given area. (From Concise Dictionary of Biology, 1990) It includes the yield of vegetative mass produced from any given crop. [MeSH:D018533] C6 zinc cluster Zinc finger motif of GAL4-type. Six cysteine residues coordinate two zinc ions, i. e. two of the thiol groups coordinate two zinc ions (six cysteines binuclear cluster DNA-binding domain). All GAL4-type proteins possess a single N-terminal zinc finger with an adjacent basic region, which is critical for sequence-specific recognition. Each C3-repeat unit of the structural motif of six cysteines forms short alpha-helical structures separated by a loop with a proline-associated turn. The zinc(II)-binding cluster lies in the DNA major groove and contacts three base pairs. (modified from [TRANSFAC:C0005] C6 zinc cluster transcription factor A transcription factor containing C6 zinc cluster domain carbohydrate A class of organic compounds containing carbon, hydrogen and oxygen and having the general formula Cm(H2O)n. They usually serve as a major energy source in the diet of animals. Example: sugar or starch. CHEBI:23008 carbohydrate IMR:0001657 carbohydrate carbon catabolite A carbon compound produced in catabolism. catabolic pathway 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. [GO:0009056] GO:0009056 catabolic process 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. [GO:0003824] GO:0003824 catalytic activity cell The fundamental, structural, and functional units or subunits of living organisms. They are composed of CYTOPLASM containing various ORGANELLES and a CELL MEMBRANE boundary. [MeSH:D002477] cell adhesion 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. [GO:0007155] cell aging Progression of the cell from its inception to the end of its lifespan. [GO:0007569] GO:0007569 cell aging cell communication 2 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. [GO:0007154] GO:0007154 cell communication cell component GO:0005575 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. [GO:0005575] cell cycle 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. [GO:0007049] cell cycle phase GO:0022403 cell cycle phase A cell cycle process comprising the steps by which a cell progresses through one of the biochemical and morphological phases and events that occur during successive cell replication or nuclear replication events. [GO:0022403] cell cycle phase transition Progression from a cell cycle phase to another cell cycle phase. cell death GO:0008219 cell death The specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. [GO:0008219] cell differentiation GO:0030154 cell differentiation The process whereby 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. [GO:0030154] cell division GO:0051301 cell division The process resulting in the physical partitioning and separation of a cell into daughter cells. [GO:0051301] cell fate determination GO:0001709 cell fate determination Process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment. [GO:0001709] cell growth GO:0016049 cell growth The process by which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. [GO:0016049] cell homeostasis GO:0019725 cellular homeostasis The processes involved in the maintenance of an internal equilibrium at the level of the cell. [GO:0019725] cell motility Any process involved in the controlled movement of a cell. [GO:0006928] GO:0006928 cell motility cellular component organization and biogenesis A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a cellular component; includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. [GO:0016043] GO:0016043 cellular component organization and biogenesis 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. [GO:0048869] GO:0048869 cellular developmental process cellular metabolic process GO:0044237 cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. [GO:0044237] cellular process GO:0009987 cellular process Processes 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:0009987] chemical IMR:0000947 chemical chromatin The material of chromosomes. It is a complex of DNA, histones, and nonhistone proteins found within the nucleus of a cell. [MeSH] chromatin silencing GO:0006342 chromatin silencing Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin. [GO:0006342] chromosomal DNA chromosome A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. [GO:0005694] GO:0005694 chromosome chronological cell aging The process associated with progression of the cell from its inception to the end of its lifespan that occurs when the cell is in a non-dividing, or quiescent, state. [GO:0001300] GO:0001300 chronological cell aging circadian GO:0007623 circadian rhythm Any biological process in an organism that recurs with a regularity of approximately 24 hours. [GO:0007623] cleavage Covalent bond breakage in a molecule leading to the formation of smaller molecules. [IEV:0002571] coiled chromosomal DNA The tightly coiled DNA contained in chromosome. cold shock domain ��A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic single-strand nucleic-acid binding proteins. This domain, which is known as the 'cold-shock domain' (CSD)...[InterPro: IPR011129] cold shock domain transcription factor A transcription factor containing cold shock domain. complex molecular entity 2 A complex form of molecular entity. complex of protein and DNA A macromolecular complex containing both protein and DNA molecules. [GO:0032993] GO:0032993 protein-DNA complex complex of protein and RNA complex regulation of transcription A combination of positive and negative regulation of transcription conformation The structural arrangement. continuant Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. [http://www.ifomis.org/bfo/1.1/light/span#Continuant] copper-fist domain A domain, similar in structure to metallothionein, undergoing a large conformational change on copper-binding that allows DNA-binding. It contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet. Conserved residues form a basic patch that may be important for DNA binding. (modified from [InterPro: IPR001083]) copper fist transcription factor Some fungal transcription factors contain an N-terminal domain, the copper fist, which seems to be involved in copper-dependent DNA-binding. These proteins activate the transcription of the metallothionein gene in response to copper. Metallothionein maintains copper levels in yeast. The copper fist domain, which is similar in structure to metallothionein itself, undergoes a large conformational change on copper-binding that allows DNA-binding. The domain contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet. Conserved residues form a basic patch that may be important for DNA binding. [InterPro: IPR001083] CG island CpG island Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes. [SO:0000307] SO:0000307 CpG_island DB domain of nuclear receptor The DNA binding domain of nuclear receptor, a group of proteins function in nuclei to regulate the transcription of target genes in a ligand-responsive manner. DM domain This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans. In D. melanogaste the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences. The NMR analysis of the DSX DM domain revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence. [InterPro: IPR001275] DM-domain-containing transcription factor A transcription factor containing DM domain. DNA A chain of deoxyribonucleotides. DNA binding domain of protein Any protein motif that binds to double- or single-stranded DNA with affinity to a specific sequence or set thereof or a general affinity to DNA. [http://en.wikipedia.org/wiki/DNA-binding_domain] DNA binding domain of transcription factor A domain of a transcription factor that binds DNA. DNA binding site A region on a molecule that recognizes and forms a chemical bond with DNA. DNA fragment A piece of DNA. DNA modification GO:0006304 DNA modification The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties. [GO:0006304] DNA molecule A chain of deoxyribonucleotides as it occures at a whole. DNA polymerase An enzyme that catalyses the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA/or RNA template or primer (modified from [GO:0003887, GO:0003964]) GO:0003887 DNA-directed DNA polymerase activity GO:0003964 RNA-directed DNA polymerase activity DNA protein interaction Any complex that forms between a protein molecule and DNA. [http://cancerweb.ncl.ac.uk/cgi-bin/omd?DNA-protein+interaction] DNA region A chain of deoxyribonucleotides that is part of a longer chain of deoxyribunucleotides. ds siRNA Double-stranded siRNA. 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. [GO:0016265] GO:0016265 death decrease negative A process of becoming smaller, less numerous, less important, or less likely. deoxynucleoside A molecule composed of a nitrogenous base attached to the five-carbon sugar deoxyribose. [http://cancerweb.ncl.ac.uk/cgi-bin/omd?deoxynucleoside] deoxynucleotide A chemical compound that consists of 3 portions: a nitrogenous base, a sugar, and one or more phosphate groups. In the most common nucleotides the base is a derivative of purine or pyrimidine, and the sugar is deoxyribose. (modified from [http://en.wikipedia.org/wiki/Deoxynucleotide#Nucleotide_structure]) deoxyribose CHEBI:28816 2-deoxy-D-ribose Deoxyribose is an aldopentose — a monosaccharide containing five carbon atoms, and including an aldehyde functional group in its linear structure. [http://en.wikipedia.org/wiki/Deoxyribose] destabilization Any process that decreases the stability. developmental process A biological process whose specific outcome is the progression of an integrated living unit: a cell, tissue, organ, or organism over time from an initial condition to a later condition. [GO:0032502] GO:0032502 developmental process dimerization GO:0046983 protein dimerization activity The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. [GO:0046983] direction The spatial relation between one point and another point. disease A definite pathologic process with a characteristic set of signs and symptoms. It may affect the whole body or any of its parts, and its etiology, pathology, and prognosis may be known or unknown. [MeSH:D004194] dosage compensation GO:0007549 dosage compensation Compensating for the two-fold variation in X:autosome chromosome ratios between sexes by a global activation or inactivation of all, or most of, genes on one or both of the X chromosomes. [GO:0007549] double strand DNA Double stranded DNA molecules downstream regulatory sequence A sequence located in the downstream region of a gene that controls the rate or manner in which the gene is expressed. elongation enhancer A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. [SO:0000165, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] SO:0000165 enhancer enhancer binding transcription factor A transcription factor selectively interacting with the enhancer enhancesome Regulatory proteins bound to DNA. enzyme A protein that has catalytic activity. epigenetic Changes in gene expression caused by mechanisms other than changes in the underlying DNA sequence. These changes may remain through cell divisions for the remainder of the cell's life and may also last for multiple generations. Adapted from wikipedia.org/wiki/Epigenetics. [nif_unclassified:nlx_200905_509] Escherichia coli E.coli NCBI Taxonomy ID: 562 Escherichia coli euchromatin Transcriptionally active form of chromatin. eukaryote NCBI Taxonomy ID: 2759 Eukaryota Organism characterized by the presence of a nucleus. Also other organelles such as mitochondria and/or chloroplasts may be present in eukaryotes. Includes all plants, animals, green algae, and fungi. [http://www.knowledgebank.irri.org/glossary/Glossary/E.htm] eukaryotic cell A cell containing a nucleus, in which the genes or DNA is housed. The eukaryotic cell has a complex internal structure and is capable of building multicellular organisms. (modified from [http://www.inproteo.com/nwglosde.html and http://www2.wwnorton.com/college/geo/earth2/glossary/e.htm] eukaryotic gene expression A process of producing a protein from its gene via transcription and translation in eukaryotes. It is usually controlled at various points in the sequence leading to protein synthesis. eukaryotic RNA polymerase promoter A DNA sequence in eukaryotic DNA to which RNA polymerase binds, to begin transcription. [SO] exon A region that codes for portion of spliced messenger RNA (SO:0000234); may contain 5'-untranslated region (SO:0000204), all open reading frames (SO:0000236) and 3'-untranslated region (SO:0000205). [SO:0000147, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] SO:0000147 exon exon on DNA Any region of DNA within a gene that is transcribed to the final messenger RNA (mRNA) molecule, rather than being spliced out from the transcribed RNA molecule. [http://en.wikipedia.org/wiki/Exon] exon on RNA The parts of a transcript (i.e. exons) that are spliced together to become mRNA or structural RNA. experimental intervention experimental method The use of controlled observations and measurements to test hypotheses. [http://wordnet.princeton.edu/perl/webwn?s=experimental%20method] expression profiling The use of high-throughput methods (e.g. DNA microarrays) for evaluating the level and timing of gene expression in a biologic sample (a cell or tissue). feedback loop The regulatory circuits whereby some proportion of the output signal of a system is passed (fed back) to the input. e.g. repressor and activator proteins in genetic operons are used to create feedback loop. forkhead/winged-helix domain The fork head protein of Drosophila melanogaster, a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors. Instead, it contains a distinct type of DNA-binding region, containing around 100 amino acids, which has since been identified in a number of transcription factors (including D. melanogaster FD1-5, mammalian HNF-3, human HTLF, Saccharomyces cerevisiae HCM1, etc.). This is referred to as the fork head domain but is also known as a 'winged helix'. The fork head domain binds B-DNA as a monomer, but shows no similarity to previously identified DNA-binding motifs. Although the domain is found in several different transcription factors, a common function is their involvement in early developmental decisions of cell fates during embryogenesis [InterPro: IPR001766] forkhead/winged-helix transcription factor A transcription factor containing forkhead/winged-helix domain formation of protein DNA complex GO:0065004 protein-DNA complex assembly The aggregation and bonding together of proteins and DNA molecules to form a protein-DNA complex. [GO:0065004] formation of transcription factor complex The joining of transcription factors formation of transcription initiation complex The process that gives rise to the transcription initiation complex. formation of translation initiation complex GO:0001732 formation of translation initiation complex Joining of the large subunit, with release of IF2/eIF2 and IF3/eIF3. This leaves the functional ribosome at the AUG, with the methionyl/formyl-methionyl-tRNA positioned at the P site. [GO:0001732] 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. [GO:0003674] GO:0003674 molecular function fungus Any of numerous microorganisms of the kingdom Fungi, which are characterized by the absence of chlorophyll and by the presence of a rigid cell wall composed of chitin, mannans and sometimes cellulose. The kingdom includes the yeasts, molds, smuts, and mushrooms. NCBI Taxonomy ID: 4751 Fungi fusion gene 2 A hybrid gene formed from two previously separate genes. It can occur as the result of a translocation, interstitial deletion, or chromosomal inversion. The fusion of two genes is often taken as evidence that these genes have related functions [http://en.wikipedia.org/wiki/Fusion_gene] fusion of DNA regions 2 The joining of a two DNA regions. fusion of gene with regulatory DNA region The joining of a gene and a regulatory DNA region. fusion of gene with reporter gene The joining of a gene and a reporter gene fusion protein The joining of two or more genes which originally coded for separate proteins. Translation of this fusion gene results in a single polypeptide with function properties derived from each of the original proteins. [http://en.wikipedia.org/wiki/Fusion_protein] G1-phase GO:0051318 G1 phase A cell cycle process comprising the steps by which a cell progresses through G1 phase, one of two 'gap' phases in the cell cycle; G1 is the interval between the completion of DNA segregation (usually by mitosis or meiosis) and the beginning of DNA synthesis. [GO:0051318] G1-S phase Progression from G1 phase to S phase of cell cycle. G2-phase A cell cycle process comprising the steps by which a cell progresses through G2 phase, one of two 'gap' phases in the cell cycle; G2 is the interval between the completion of DNA synthesis and the beginning of DNA segregation (usually by mitosis or meiosis). [GO:0051319] GO:0051319 G2 phase G2-M phase Progression from G2 phase to M phase of cell cycle. GCM domain A domain containing many conserved basic amino acid residues, seven cysteine residues, and four histidine residues. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. (modified from [InterPro:IPR003902]) glia cell missing transcription factors GCM transcription factor GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3'. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding. ! gas IMR:0001720 gas The vapor state of matter; nonelastic fluids in which the molecules are in free movement and their mean positions far apart. Gases tend to expand indefinitely, to diffuse and mix readily with other gases, to have definite relations of volume, temperature, and pressure, and to condense or liquefy at low temperatures or under sufficient pressure. [IMR:0001720, MeSH:D005740] gene A unit of inheritance; a working subunit of DNA that contributes to phenotype/function and carries a particular set of instructions, usually coding for a particular protein. SO:0000704 gene gene expression The process by which the information encoded in a gene is converted into protein or some form of RNA. The DNA sequence is first transcribed into RNA and then usually translated into protein. [http://www.homepages.indiana.edu/120800/text/glossary.html] gene expression regulator gene fusion 2 The accidental joining of DNA of two genes, such as can occur in a translocation or inversion. Gene fusions can give rise to hybrid proteins or to the misregulation of the transcription of one gene by the cis regulatory elements (enhancers) of another. [http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-G/gene_fusion.html] gene mutation A change or alteration in a gene. gene product The biochemical material, either RNA or protein, resulting from expression of a gene. [http://en.wikipedia.org/wiki/Gene_product] gene product function GO:0003674 molecular function gene region A region that harbors a gene. gene regulation pathway A pathway that controls the rate or manner in which a gene is expressed. gene silencing GO:0016458 gene silencing Any transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation. [GO:0016458] general transcription factor A transcription factor that is required to initiate all transcription events independent of upstream regulatory elements.[PANTHER:MF00228] basal transcription factor genetic imprinting GO:0071514 genetic imprinting Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules by a mechanism that is mediated by DNA, is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence. [GO:0071514] genetic modification grainy-head transcription factor A transcription factor containing grainy-head motif. grainyhead A domain of 250 amino acid residues which is required for binding to DNA and a C-terminal dimerization domain. It has a basic helix-loop-helix motif and a isoleucine-rich activation motif. growth GO:0040007 growth The increase in size or mass of an entire organism, a part of an organism or a cell. [GO:0040007 ] HMG A DNA-binding domain which in some instances such as HMG1 mediates sequence-unspecific, in other cases such LEF-1 sequence-specific binding to DNA. This domain exhibits a typical L-shaped conformation made up of 3 alpha-helices and an extended N-terminal extension of the first helix. The latter together with helix 1, which contains a kink, form the long arm of the L, whereas helices 1 and 2 form the short arm. Binding to the minor groove induces a sharp bending of the DNA by more than 90 degree, away from the bound protein. The overall topology of the DNA-protein complexes resembles somewhat that of the TBP-TATA box complex. (modified from [TRANSFAC:C0015]) HMG-box transcription factor A transcription factor containing high mobility group protein (HMG) box. [PANTHER:MF00226] HSF domain Heat shock factor (HSF) is a transcriptional activator of heat shock genes: it binds specifically to heat shock promoter elements, which are palindromic sequences rich with repetitive purine and pyrimidine motifs. Under normal conditions, HSF is a homo-trimeric cytoplasmic protein, but heat shock activation results in relocalisation to the nucleus. Each HSF monomer contains one C-terminal and three N-terminal leucine zipper repeats. Point mutations in these regions result in disruption of cellular localisation, rendering the protein constitutively nuclear. Two sequences flanking the N-terminal zippers fit the consensus of a bi- partite nuclear localisation signal (NLS). Interaction between the N- and C-terminal zippers may result in a structure that masks the NLS sequences: following activation of HSF, these may then be unmasked, resulting in relocalisation of the protein to the nucleus. The DNA-binding component of HSF lies to the N-terminus of the first NLS region, a! HSF transcription factor Heat shock transcription factor helix-turn-helix domain A domain containing two helices connected by a short turn. The second helix binds to DNA with the helix in the major groove, which allows the contact between specific base and residues throughout the protein. The HtH domain is found primarily in gene regulatory proteins and binds DNA in a sequence specific manner. helix-turn-helix domain transcription factor A transcription factor containing helix-turn-helix domain. heterochromatin Transcriptionally inactive form of chromatin. heterocyclic base A chemical structure containing a heterocyclic ring. A heterocyclic base unit in each nucleotide (either a pyrimidine or a purine) has nitrogen within the rings so also called a nitrogenous base. heterodimerization GO:0046982 protein heterodimerization activity Interacting selectively with a nonidentical protein to form a heterodimer. [GO:0046982] histone Any of five related proteins, composed primarily of basic amino acids, which are the scaffold around which DNA is wound to form the chromatin structure of eukaryotic chromosomes [http://www.accessexcellence.org/AE/AEPC/WWC/1994/glossary.html] histone acetylation GO:0016573 histone acetylation The modification of histones by addition of acetyl groups. [GO:0016573] histone fold A motif consisting of a core of three helices, where the long middle helix is flanked at each end by shorter ones. Proteins displaying this structure include the nucleosome core histones, which form octomers composed of two copies of each of the four histones, H2A, H2B, H3 and H4; archaeal histone, which possesses only the core domain part of eukaryotic histone; and the TATA-box binding protein (TBP)-associated factors (TAF), where the histone fold is a common motif for mediating TAF-TAF interactions. TAF proteins include TAF(II)18 and TAF(II)28, which form a heterodimer, TAF(II)42 and TAF(II)62, which form a heterotetramer similar to (H3-H4)2, and the negative cofactor 2 (NC2) alpha and beta chains, which form a heterodimer. (modified from [InterPro:IPR009072]) histone fold transcription factor A transcription factor containing structure of histone fold. holoenzyme A complete and catalytically active enzyme consisting of all subunits. (i.e. Holoenzyme = Apoenzyme + Cofactor). homeo box Three consecutive alpha-helix structures, helix 3 contacts mainly the major groove of the DNA, some contacts at the minor groove are observed as well. Helix 2 and 3 resemble the helix-turn-helix structure of prokaryotic regulators. [TRANSFAC:C0006] homeobox transcription factor A transcription factor containing the homeobox domain. It is usually involved in the control of gene expression during morphogenesis and development. [PANTHER:MF00038] homodimerization GO:0042803 protein homodimerization activity Interacting selectively with an identical protein to form a homodimer. [GO:0042803] housekeeping gene A gene involved in basic functions needed for the sustenance of the cell. Housekeeping genes are constitutively expressed (they are always turned ON). [http://www.medterms.com/script/main/art.asp?articlekey=24232] increase positive A process of becoming larger, more numerous, more important, or more likely. [NCI:C25533] NCI:C25533 Increase information biopolymer Naturally occurring macromolecules that harbor biological information in their structures, e.g. proteins, nucleic acids. inhibition negative Any process that stops, prevents or reduces the frequency, rate or extent of an action. inorganic chemical inositol phosphate CHEBI:24846 inositol phosphates instrument A device for measuring, recording, or controlling insulator Prevents eukaryotic gene regulatory proteins from influencing distant genes / a trancriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression. [] SO:0000627 insulator boundary element insulator element interphase GO:0051325 interphase A cell cycle process comprising the steps by which a cell progresses through interphase, the stage of cell cycle between successive rounds of chromosome segregation. Canonically, interphase is the stage of the cell cycle during which the biochemical and physiologic functions of the cell are performed and replication of chromatin occurs. [GO:0051325] intra cellular process Processes that are carried out within the cell intracellular transport GO:0046907 intracellular transport The directed movement of substances within a cell. [GO:0046907] intra organismal process The biological processes occurring inside the organism. intron A segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it. [SO: 0000188, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] SO:0000188 intron intron on DNA A non-coding segment of DNA; edited out during the transcription process. [http://library.thinkquest.org/17109/glossary.htm] intron on RNA The parts that are transcribed along with the exons but are removed from the primary gene transcript (pre-RNA) by RNA SPLICING to leave mature RNA. ion An ion is a molecular entity having a net electric charge. [CHEBI:24870] CHEBI:24870 ions IMR:0001658 ion ligand Binding to a specific receptor protein and activating intracellular signaling cascades that alter the behavior of the cell. [IMR:0000002, ISBN:0815340729] IMR:0000002 ligand lipid A loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. [CHEBI:18059] CHEBI:18059 lipids IMR:0000947 lipid living entity An entity of a living organism (a life form). localization Any process by 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. [GO:0051179] GO:0051179 localization locus The position of a gene (or other chromosome marker) on a chromosome. LCR A region that enhances the expression of linked genes to physiological levels in a tissue-specific and copy number-dependent manner at ectopic chromatin sites. It is required for normal regulation of expression of some genes. SO:0000037 locus control region locus control region long siRNA MADS Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box, that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit.! MADS transcription factor A transcription factor containing MADS domain. maintenance major groove In a helix, refers to the larger of the unequal grooves that are formed as a result of the double-helical structure of DNA. As a result of the patterns of hydrogen bonding between complementary bases of DNA, the sugar groups stick out at 120 degree angles from each other instead of 180. The major groove is generated by the larger angular distance between sugars. [http://www.sparknotes.com/biology/molecular/structureofnucleicacids/terms/term_11.html] meiosis GO:0007126 meiosis A cell cycle process comprising the steps by which a cell progresses through the nuclear division phase of a meiotic cell cycle, the specialized nuclear and cell division in which a single diploid cell undergoes two nuclear divisions following a single round of DNA replication in order to produce four daughter cells that contain half the number of chromosomes as the diploid cell. Meiotic division occurs during the formation of gametes from diploid organisms and at the beginning of haplophase in those organisms that alternate between diploid and haploid generations. [GO:0007126] messenger RNA A type of RNA that reflects the exact nucleoside sequence of the genetically active DNA. mRNA carries the message of the DNA to the cytoplasm of cells where protein is made in amino acid sequences specified by the mRNA. [http://www.ehsc.orst.edu/outreach/glossary.html] mRNA metabolic pathway GO:0008152 metabolic process Processes that cause many of the chemical changes in living organisms, including anabolism and catabolism. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. [GO:0008152] methylation GO:0032259 methylation The process by which a methyl group is covalently attached to a molecule. [GO:0032259] miRNA Single-stranded RNA molecules of about 21-23 nucleotides in length, which regulate gene expression. miRNAs are encoded by genes that are transcribed from DNA but not translated into protein (non-coding RNA); instead they are processed from primary transcripts known as pri-miRNA to short stem-loop structures called pre-miRNA and finally to functional miRNA. Mature miRNA molecules are partially complementary to one or more messenger RNA (mRNA) molecules, and their main function is to downregulate gene expression. [http://en.wikipedia.org/wiki/MicroRNA] microRNA microorganism An organism that can be seen only through a microscope. Microorganisms include bacteria, protozoa, algae, and fungi. Although viruses are not considered living organisms, they are sometimes classified as microorganisms. [http://www.stjude.org/stjude/hospital/med_terms.jsp?medterm=M] minor groove In a helix, refers to the smaller of the unequal grooves that are formed as a result of the double-helical structure of DNA. As a result of the patterns of hydrogen bonding between complementary bases of DNA, the sugar groups stick out at 120 degree angles from each other instead of 180. The minor groove is generated by the smaller angular distance between sugars. [http://www.sparknotes.com/biology/molecular/structureofnucleicacids/terms/term_12.html] 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. [GO:0005739] GO:0005739 mitochondrion mitosis 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. [GO:0007067] GO:0007067 mitosis modification modification of molecular entity A process that causes a change (e.g. covalent alteration or a change of activity) of molecular entity. molecular binding Interacting selectively with molecules molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. [http://en.wikipedia.org/wiki/Molecular_entity] 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. [GO:0003674] GO:0003674 molecular function molecular interaction Interaction of a molecule with another molecule. molecular process Any processes that are carried out at the molecular level. molecular structure The arrangement of atoms in a molecule. motif identification Identification of motifs using the experimental and computational techniques. mutant gene A gene that has changed (e.g. lost, gained, or exchanged some of the material it received from its parent), affecting the normal transmission and expression of a trait. mutant protein mutant regulatory DNA mutated protein A protein having a change in its amino acid sequence caused by a mutation. mutation A permanent change in the DNA sequence of a gene that alters the genetic message carried by that gene. ncRNA non-coding RNA negative regulation negative The process by which a cell decreases the number of a cellular component, such as RNA or protein, in response to an external variable. [http://en.wikipedia.org/wiki/Downregulation] down regulation negative regulation of gene expression negative Any process that stops, prevents or reduces the frequency, rate or extent of gene expression. negative regulation of transcription negative Any process that stops, prevents or reduces the frequency, rate or extent of transcription. [GO:0016481] GO:0016481 negative regulation of transcription negative regulation of transcription by transcription repressor Any process involving transcription repressor activity that stops, prevents or reduces the rate of transcription (modified from [GO:0016481]). negative regulation of transcription of gene negative negative regulation of translation negative Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GO:0017148] GO:0017148 negative regulation of protein biosynthetic process negative transcription regulator Any transcription regulator that prevents or downregulates transcription. non physical continuant A non physical continuant is an entity that has no spatial dimension and no mass . nuclear export of mRNA GO:0006406 mRNA export from nucleus The directed movement of mRNA from the nucleus to the cytoplasm. [GO:0006406] nuclear receptor transcription factor A ligand-dependent receptor found in the nucleus of the cell. [GO:0004879] GO:0004879 ligand-dependent nuclear receptor activity nucleic acid CHEBI:33696 nucleic acids Macromolecules, the major organic matter of the nuclei of biological cells, made up of nucleotide units, and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. [CHEBI:33696] nucleic acid molecule A complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are found in all living cells and viruses. [http://en.wikipedia.org/wiki/Nucleic_acid] nucleic acid region A sequence feature of nucleic acids. nucleoside CHEBI: 33838 nucleosides IMR:0001697 nucleoside Ribosyl or deoxyribosyl derivatives of the pyrimidine or purine bases adenine, guanine, xanthine, thymine, cytosine, and uracil. [CHEBI: 33838] nucleosome Spherical sub-units of eukaryotic chromatin that are composed of a core particle consisting of an octamer of histones (two molecules each of histones H2a, H2b, H3 and H4) and 146 nucleotide pairs. [http://www.fao.org/docrep/003/X3910E/X3910E17.htm] nucleotide A nucleotide consists of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups. Nucleotides can carry chemical energy (e.g. ATP), form coenzymes (e.g. CoA), be used as specific signaling molecules (e.g. cAMP) in the cell. Nucleotides are the subunits of the nucleic acids. [IMR:0001349, ISBN:0815340729] CHEBI:25608 nucleoside phosphates IMR:0001349 nucleotide 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. [GO:0005634] GO:0005634 nucleus occurrent An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants. [http://www.ifomis.org/bfo/1.1/light/span#Occurrent] ORF SO:0000236 ORF The inframe interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER. [SO:0000236] open reading frame operator A regulatory element of an operon to which activators or repressors bind hereby effecting translation of genes in that operon. [SO:0000057] SO:0000057 operator operon A genetic regulatory system in which genes (structural genes) coding for functionally related proteins are clustered along the DNA. The expression of structural genes is controlled by the regulatory elements (operator genes) that respond to environmental cues. SO:0000178 operon organic chemical organism An individual living system (such as animal, plant, fungus or micro-organism). In at least some form, all organisms are capable of reacting to stimuli, reproduction, growth and maintenance as a stable whole (after FAO[1]). An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. [http://en.wikipedia.org/wiki/Organism] organismal process GO:0032501multicellular organismal process The biological processes, occurring at the level of the organism, pertinent to the function of the organism. [GO:0032501] orientation A position or arrangement of points, relative to one another or other specific directions. osmotic stress An increase or decrease in the concentration of solutes outside the organism or cell (modified from [GO:0006970]). oxidative stress A state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals (modified from [GO:0006979]). packed DNA A packed form of DNA. paired box A domain consisting of a conserved 124 amino acid N-terminal sequence, found in several developmentally regulated proteins in fruit fly, mouse and human paired box transcription factor A transcription factor containing paired box domain, found in several developmentally regulated proteins in fruit fly, mouse and human pathway A series of related biochemical reactions. [http://www.genpromag.com/Glossary.aspx] peptide phenotype Any observed quality of an organism, such as its morphology, development, or behavior, as opposed to its genotype - the inherited instructions it carries, which may or may not be expressed. [http://en.wikipedia.org/wiki/Phenotype] phosphate group CHEBI:32958 phosphate group phosphorylation GO:0016310 phosphorylation The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [GO:0016310] physical contact Physically touching of two or more objects. physical continuant A physical continuant is an entity that has spatial dimension. It can either have mass (such as a protein) or no mass (such as DNA minor groove). physical interaction An action that occurs as two or more objects have a physical effect upon one another. (modified from [http://en.wikipedia.org/wiki/Physical_interaction]) biological process GO:0008150 biological process Those processes 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:0008150] physiological process physiological process phase plant Multicellular, eukaryotic life forms of the kingdom Plantae. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions ( MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alteration of haploid and diploid generations. [MESH:D010944] NCBI Taxonomy ID:3193 Embryophyta pocket domain pocket consists of two conserved 'boxes' (A and B) with a less conserved spacer region lying in between pocket domain transcription factor A transcription factor containing pocket domain (e.g. the RB protein). poly-A signal sequence SO:0000551 polyA signal sequence The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. [SO:0000551, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] polymerase Enzymes that catalyze the synthesis of nucleic acids on preexisting nucleic acid templates, assembling RNA from ribonucleotides or DNA from deoxyribonucleotides. [http://www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html#p] polymerase activity Catalysis of the reaction that synthesizes nucleic acids on preexisting nucleic acid templates, assembling RNA from ribonucleotides or DNA from deoxyribonucleotides positive regulation positive Any process that activates or increases the frequency, rate or extent of a biological process, function or phenomenon. up regulation positive regulation of gene expression positive Any process that activates or increases the frequency, rate or extent of gene expression. positive regulation of transcription positive Any process that activates or increases the frequency, rate or extent of transcription. [GO:0045941] GO:0045941 positive regulation of transcription positive regulation of transcription by transcription activator Any process involving transcription activator activity that activates or increases the frequency, rate or extent of transcription (modified from [GO:0045941]). positive regulation of transcription of gene positive positive regulation of translation positive Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GO:0045727] GO:0045727 positive regulation of protein biosynthetic process positive transcription regulator A transcription regulator activity required for initiation or upregulation of transcription. posttranscriptional Any substance or process that is formed or occurs after the production of a mRNA transcript. posttranscriptional modification A genetic process by which, in eukaryotic cells, primary transcript RNA is converted into mature RNA. The three main modifications are 5' capping, 3' polyadenylation, and RNA splicing. (modified from [http://en.wikipedia.org/wiki/Post-transcriptional_modification]) posttranslational Any substance or process that is formed or occurs after translation of protein. posttranslational modification GO:0043687 post-translational protein modification The covalent alteration of one or more amino acids occurring in a protein after the protein has been completely translated and released from the ribosome. [GO:0043687] pre-miRNA A stem loop intermediate (60-70 nucleotide) in microRNA production, produced by the nuclear cleavage of a primary miRNA (pri-mRNA) transcript. Pre-microRNAs are transported from the nucleus to the cytoplasm where further cleavage occurs to produce a mature microRNA product (modified from [GO:0035281]). pre-microRNA primary structure (Wikipedia, en:) The primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including stereochemistry). For a typical unbranched, un-crosslinked biopolymer (such as a molecule of DNA, RNA or typical intracellular protein), the primary structure is equivalent to specifying the sequence of its monomeric subunits, e.g., the nucleotide or peptide sequence. process 1 A process is a collection of molecular events with a defined beginning and end. [GO:0008150] GO:0008150 biological process producing prokaryote Cell or organism lacking a membrane-bound, structurally discrete nucleus and other subcellular compartments. Bacteria are prokaryotes. [http://www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html#p] promoter A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. [SO:0000167] SO:0000167 promoter protein a macromolecule composed of one or several polypeptides. Each polypeptide consists of a chain of amino acids linked together by covalent (peptide) bonds. [http://www.qimr.edu.au/qimr_glossary.html] protein amplification Amplification of protein from a pool of mRNA using technologies such as phage display and Profusion technology. protein binding site of DNA A region on DNA that specifically forms a chemical bond with a protein (or proteins). protein binding site of protein A region on a protein that forms a chemical bond (protein ligands) with other proteins. protein biosynthesis The chemical reactions and pathways resulting in the formation of proteins. protein catabolism GO:0030163 protein catabolic process The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. [GO:0030163] protein coding DNA region A DNA region that encodes one or more proteins.. protein coding gene A gene that encodes a protein protein coding region protein complex 2 Any protein group composed of two or more subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups. [GO:0043234] GO:0043234 protein complex protein domain A part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural domains. [http://en.wikipedia.org/wiki/Structural_domain] protein folding GO:0006457 protein folding The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure. [GO:0006457] protein identification Identification of proteins using the techniques of electrophoresis, mass spectrometry, etc. protein maturation GO:0051604 protein maturation The process leading to the attainment of the full functional capacity of a protein. [GO:0051604] protein metabolism GO:0019538 protein metabolic process The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification. [GO:0019538] protein modification GO:0006464 protein modification process The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). [GO:0006464] protein mutation A mutation that alters the protein product of a gene. protein polymerization GO:0051258 protein polymerization The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein. [GO:0051258] protein protein interaction the association of protein molecules and the study of these associations from the perspective of biochemistry, signal transduction and networks. [http://en.wikipedia.org/wiki/Protein-protein_interaction] protein subunit A single protein molecule that assembles (or coassembles) with other protein molecules to form a multimeric or oligomeric protein. [http://en.wikipedia.org/wiki/Protein_subunit] protein targeting GO:0006605 protein targeting The process of targeting specific proteins to particular membrane-bound subcellular organelles. Usually requires an organelle specific protein sequence motif. [GO:0006605] protein transport GO:0015031 protein transport The directed movement of proteins into, out of, within or between cells. [GO:0015031] protist A single-celled, eukaryotic organism that may resemble an animal or a plant. (Allaby 1998) [http://www.oup.com.au/orc/demo_glossary.aspx#P] quality RHR A DNA binding domain (Rel-type) exhibiting a bipartite subdomain structure, each subdomain comprising a beta-barrel with five loops that form an extensive contact surface to the major groove of the DNA. Particularly, the first loop of the N-terminal subdomain (the highly conserved recognition loop) performs contacts with the recognition element on the DNA, but other loops are involved. The second, C-terminal domain is necessary mainly for protein dimerization. (modified from [TRANSFAC:C0020]) RHR transcription factor A transcription factor containing RHR domain RNA A chain of ribonucleotides. RNA biosynthesis GO:0032774 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. [GO:0032774] RNA catabolism GO:0006401 RNA catabolic process The chemical reactions and pathways resulting in the breakdown 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. [GO:0006401] RNA coding DNA region A region on DNA that encodes RNA. RNA coding gene A gene coding for RNA (tRNA, rRNA, etc.). RNA coding region RNA elongation GO:0006354 RNA elongation The extension of an RNA molecule after transcription initiation by the addition of ribonucleotides catalyzed by an RNA polymerase. [GO:0006354] RNA initiated silencing complex A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation. [GO:0016442] GO:0016442 RNA-induced silencing complex RNA interference GO:0016246 RNA interference The process by which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes. [GO:0016246] RNA metabolism GO:0016070 RNA metabolic process The 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. [GO:0016070] RNA modification GO:0009451 RNA modification The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically. [GO:0009451] RNA molecule A chain of ribonucleotides as it occures at a whole. RNA polymerase An enzyme that catalyses the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA or RNA template (modified from [GO:0003899, GO:0003968]). GO:0003899 DNA-directed RNA polymerase activity GO:0003968 RNA-directed RNA polymerase activity RNA polymerase activity Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA or RNA template (modified from [GO:0003899, GO:0003968]). GO:0003899 DNA-directed RNA polymerase activity; GO:0003968 RNA-directed RNA polymerase activity RNA polymerase binding site of DNA A region on DNA that specifically forms a chemical bond with RNA polymerase. RNA polymerase II An enzyme found in eukaryotic cells that catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. Also called RNAP II and Pol II. RNA polymerase II holoenzyme GO:0016591 DNA-directed RNA polymerase II, holoenzyme Large protein complex composed of the RNA polymerase core complex and a variety of other proteins including transcription factor complexes TFIIA, D, E, F, and H which are required for promoter recognition, and the Mediator subcomplex. Catalyzes the synthesis of eukaryotic pre-mRNA. [GO:0016591] RNAPolymerase promoter A region (DNA) to which RNA polymerase binds, to begin transcription. [SO:0001203] SO:0001203 RNA_polymerase_promoter RNA polymerase III promoter A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription. [SO:0000171] SO:0000171 RNApol III promoter RNA polymerase III promoter type 1 SO:0000617 RNApol_III_promoter_type_1 RNA polymerase III promoter type 2 SO:0000618 RNApol_III_promoter_type_2 RNA polymerase II promoter A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription. [SO:0000170] SO:0000170 RNApol II promoter RNA polymerase I promoter A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription. [SO:0000169] SO:0000169 RNApol I promoter RNA processing Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. [GO:0006396] GO:0006396 RNA processing RNA protein interaction GO:0022618 protein-RNA complex assembly The aggregation and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. [GO:0022618] RNA region A chain of ribonucleotides that is part of a longer chain of ribunucleotides. RNA splicing GO:0008380 RNA splicing The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA. [GO:0008380] regulation of function Any process that modulates the frequency, rate or extent of function. regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression. [GO:0010468] GO:0010468 regulation of gene expression regulation of metabolic process regulation of modification of molecular entity Any process that modulates the frequency, rate or extent of modification of molecular entity. regulation of pathway Any process that modulates the frequency, rate or extent of a pathway regulation of physical interaction Any process that modulates the frequency, rate or extent of physical interaction. regulation of process Any process that modulates the frequency, rate or extent of process. regulation of stability Any process that modulates the stability. regulation of transcriptin by two component regulatory system Any process that modulates the frequency, rate or extent of transcription by protein components involved in a system responding to environmental changes characterized usually by a sensor kinase in the cell membrane that phosphorylates itself in response to a signal and a response regulator to which the phosphoryl group is transferred. regulation of transcription Any process that modulates the frequency, rate or extent of the synthesis of either RNA on a template of DNA or DNA on a template of RNA. [GO:0045449] GO:0045449 regulation of transcription regulation of transcription of gene regulation of transcription of operon Any process that modulates the frequency, rate or extent of the synthesis of RNA on a template of DNA or DNA on a template of RNA. regulation of transcription of regulon Any process that modulates the frequency, rate or extent of transcription of regulon regulation of translation Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GO:0006417] GO:0006417 regulation of translation regulation of translational fidelity Any process that modulates the ability of the translational apparatus to interpret the genetic code. [GO:0006450] GO:0006450 regulation of translational fidelity regulatory sequence A DNA sequence that controls the expression of a gene. [SO:0005836, http://www.genpromag.com/scripts/glossary.asp?LETTER=R] Typically binding sites for proteins required for transcription, such as gene regulatory proteins and polymerases. SO:0005836 regulatory region regulatory DNA regulatory DNA region regulatory 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. [GO:0050789] GO:0050789 regulation of biological process regulon A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal. [SO:1001284, ISBN:0198506732] SO:1001284 regulon replicative cell aging GO:0001302 replicative cell aging The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division. [GO:0001302] reporter gene A transfected gene that encodes an easily assayed product, such as GFP; it is used to monitor gene expression under different conditions; usually to test the activity of a promoter. reporter gene construction Construction of any gene that encodes an easily assayed product that is used to monitor gene expression under different conditions; usually to test the activity of a promoter. response process GO:0050896 response to stimulus The process of changing state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.), resulting from a stimulus. [GO:0050896] (revised) response to chemical stimulus response to chemical stimulus 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. [GO:0042221] GO:0042221 response to chemical stimulus response to drug 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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease. [GO:0042493] GO:0042493 response to drug response to protein 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 protein stimulus. [GO:0051789] GO:0051789 response to protein stimulus response to protein stimulus ribose CHEBI:26564 riboses ribosomal DNA DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA. [MeSH:D004275] ribosomal gene Genes encoding ribosomal proteins and rRNAs. rRNA RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. [SO:0000252, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732] SO:0000252 rRNA ribosome GO:0005840 ribosome An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [GO:0005840] runt like domain A domain homologous to a defined region within the Drosophila protein Runt. The runt domain contains twelve beta strands, seven of which shape the fold of an immunoglobulin-like beta sandwich (S-type Ig fold) also found in the DNA-binding domains of other transcription factors (NF-kappaB, NFAT, p53, STAT, and the T-domain) that is preceded by an N-terminal alpha helix. The runt domain is responsible for both DNA-binding and heterodimerization which occur at distinct, non-overlapping sites within the domain (modified from [TRANSFAC:C0029]). runt-like transcription factor A transcription factor containing runt-like domain. runt-domain-like transcription factor SAND domain The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA bindin! SAND domain transcription factor A transcription factor containing SAND domain SMAD NF-1 transcription factor A transcription factor containing SMAD NF-1 domain SMAD NF 1 domain Two DNA binding domains (SMAD and NF1) sharing structural similarity. The SMAD (MH2) domain consists of a sandwich of eleven beta strands in two sheets with Greek key topology. SMAD proteins mediate signaling by the TGF-beta/activin/BMP-2/4 cytokines from receptor Ser/Thr protein kinases at the cell surface to the nucleus. Nuclear factor 1 (NF-1; or CCAAT box-binding transcription factor, CTF) is found in a family of vertebrate nuclear proteins which recognize and bind, as dimers, the palindromic DNA sequence 5'-TGGCANNNTGCCA-3'. The NF-1 proteins have been implicated as regulators of diverse biological processes such as adenovirus replication and transcription of TGF-responsive genes. (modified from [InterPro: IPR008984, IPR000647]) S-phase GO:0051320 S phase A cell cycle process comprising the steps by which a cell progresses through S phase, the part of the cell cycle during which DNA synthesis takes place. [GO:0051320] ss siRNA Single-stranded siRNA. STAT The structurally and functionally conserved domains shared by the STAT proteins including: an N-terminal domain that strengthens interactions between STAT dimers on adjacent DNA-binding sites; a coiled-coil STAT domain that is implicated in protein-protein interactions; a DNA-binding domain with an immunoglobulin-like fold similar to p53 tumour suppressor protein; an EF-hand-like linker domain connecting the DNA-binding and SH2 domains; an SH2 domain that acts as a phosphorylation-dependent switch to control receptor recognition and DNA-binding; and a C-terminal transactivation domain. (modified from [InterPro:IPR013801] STAT transcription factor The STAT protein (Signal Transducers and Activators of Transcription) family contains transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors, hence they act as signal transducers in the cytoplasm and transcription activators in the nucleus. Binding of these factors to cell-surface receptors leads to receptor autophosphorylation at a tyrosine, the phosphotyrosine being recognised by the STAT SH2 domain, which mediates the recruitment of STAT proteins from the cytosol and their association with the activated receptor. The STAT proteins are then activated by phosphorylation via members of the JAK family of protein kinases, causing them to dimerise and translocated to the nucleus, where they bind to specific promoter sequences in target genes. In mammals, STATs comprise a family of seven structurally and functionally related proteins: Stat1, Stat2, Stat3, Stat4, Stat5a and Stat5b, Stat6. STAT p! second messenger IMR:0100022 second messenger selenocysteine incorporation The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine. [GO:0001514] GO:0001514 selenocysteine incorporation sequence The order of nucleotides in RNA or DNA or of amino acids in a polypeptide. [http://www.plantpath.cornell.edu/glossary/Defs_S.htm] sequence homology analysis An analytic procedure that compares the similarity of a sequence with other sequences. sigma factor A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes. [GO:0016987] sigma factor activity Activity of a sigma factor. A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes. [GO:0016987] GO:0016987 sigma factor activity sigma factor antagonist activity GO:0016989 sigma factor antagonist activity The function of binding to a sigma factor and stopping, preventing or reducing the rate of its transcriptional activity. [GO:0016989] signaling pathway GO:0007165 signal transduction The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately effecting a change in the functioning of the cell. [GO:0007165] silencer Combination of short DNA sequence elements which suppress the transcription of an adjacent gene or genes. [SO:0000625, http://www.brunel.ac.uk/depts/bio/project/old_hmg/gloss3.htm] SO:0000625 silencer silencing single strand DNA DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form. Parvoviridae have a single stranded DNA genome. Single stranded DNA can be produced experimentally by rapidly cooling heat denatured DNA. Heating causes the strands to separate and rapid cooling prevents renaturation. [http://www.biology-online.org/dictionary/Single_stranded_dna] siRNA A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. [SO:0000646] SO:0000646 siRNA small interfering RNA solution A solution is a homogeneous mixture composed of two or more substances. In such a mixture, a solute is dissolved in another substance, known as a solvent. [http://en.wikipedia.org/wiki/Solution] solvent A substance (usually a liquid) that dissolves other substances to form a solution spacer A region placed between two or more pieces of sequence features (e.g. genes). Provides flexibility needed for communication between DNA bound proteins. Not recognized by gene regulatory proteins. splice enhancer Region of a transcript that regulates splicing. [SO:0000344] SO:0000344 splice enhancer spliceosome IMR:0000932 spliceosome The splicing reaction is carried out by the spliceosome, which consists of five small nuclear ribonucleoprotein complexes U1, U2, U4, U5 and U6 snRNPs and a large number of non-snRNP proteins. [IMR:0000932] splicing The process of removing sections of the sequences of a precursor RNA or protein, and joining the remaining sections to form the mature form of RNA or protein. stabilization starvation Lengthy and continuous deprivation of food. (Stedman, 25th ed) [MeSH: D013217] stimulon A set of genes/proteins under regulation by the same stimulus stress MSH2003_2003_05_12A pathological process resulting from the reaction of the body to external forces and abnormal conditions that tend to disturb the organism's homeostasis. structural domain of transcription activator A compact, globular sub-structure of a transcription activator. structural domain of transcription repressor A compact, globular sub-structure of a transcription repressor. substrate A molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate(s). The substrate binds with the enzyme's active site, and an enzyme-substrate complex is formed. The substrate is broken down into a product and is released from the active site. The active site is now free to accept another substrate molecule. [http://en.wikipedia.org/wiki/Substrate_%28biochemistry%29] TATA box A DNA sequence (cis-regulatory element) found in the promoter region of most genes in eukaryotes (also called Goldberg-Hogness box). Considered to be the core promoter sequence, it is the binding site of either transcription factors or histones (the binding of a transcription factor blocks the binding of a histone and vice versa) and is involved in the process of transcription by RNA polymerase. It has the core DNA sequence 5'-TATAAA-3' or a variant, which is usually followed by three or more adenine bases. The TATA box is usually located 25 base pairs upstream to the transcription site. (modified from [http://en.wikipedia.org/wiki/TATA_box]) TATA-binding protein TBP The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins. By contrast, the N-terminal region varies in both length and sequence. [InterPro: IPR000814] TBP domain A domain within TATA-box binding proteins. T box domain A domain defined as the minimal region within the T-box protein that is both necessary and sufficient for sequence-specific DNA binding, all members of the family bind to the DNA consensus sequence TCACACCT. Transcription factors of the T-box family are required both for early cell-fate decisions, such as those necessary for formation of the basic vertebrate body plan, and for differentiation and organogenesis. (modified from [InterPro:IPR001699] TEA domain A domain containing a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. (modified from [InterPro:IPR000818]) TEA domain transcription factor Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTS domain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism. [InterPro: IPR000818] TF binding site of protein A region on a protein that forms a chemical bond with one or more transcription factors. TF module temperature A degree of hotness or coldness the can be measured using a thermometer. Temperature is measured in degrees on the Fahrenheit, Celsius, and Kelvin scales. [http://eo.ucar.edu/webweather/glossary.html] temporal quality terminator SO:0000141 terminator The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. [SO:0000141, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] three dimensional molecular structure 3D structure of a molecule tissue A group of similar cells, specialized to perform a particular function (or functions). Examples of tissue include, heart mucslce, skin, bone etc.[http://medicineworld.org/cancer/descriptions.html] trans-acting siRNA A form of small interfering RNA (siRNA) that represses gene expression through post-transcriptional gene silencing in land plants. It is transcribed from the genome to form a polyadenylated, double-stranded precursor. Unlike other siRNAs, but like microRNA, ta-siRNA does not require full complementarity to its target RNA to have an effect. [http://en.wikipedia.org/wiki/Trans-acting_siRNA] transcript An RNA synthesized on a DNA or RNA template by an RNA polymerase. [SO:0000673] SO:0000673 transcript transcription GO:0006350 transcription The synthesis of either RNA on a template of DNA or DNA on a template of RNA. [GO:0006350] transcription activator A transcription regulator required for initiation of transcription. transcription activator activity Any transcription regulator activity required for initiation or upregulation of transcription. [GO:0016563] GO:0016563 transcription activator activity transcription coactivator A transcription cofactor that activates transcription from a RNA polymerase II promoter; it does not bind DNA itself. (modified from [GO:0003713]) GO:0003713 transcription coactivator activity transcription cofactor A transcription factor that binds to other transcription factors / the core RNA polymerase II complex but does not bind DNA itself. transcription cofactor activity GO:0003712 transcription cofactor activity The function that links a sequence-specific transcription factor to the core RNA polymerase II complex but does not bind DNA itself. [GO:0003712] transcription corepressor A transcription cofactor that represses transcription from a RNA polymerase II promoter; it does not bind DNA itself. (modified from [GO:0003714]) GO:0003714 transcription corepressor activity transcription DNA-dependent The synthesis of RNA on a template of DNA. [GO:0006351] transcription during RNA-mediated transposition GO:0032199 transcription during RNA-mediated transposition The synthesis of DNA from an RNA transposon intermediate. [GO:0032199] transcription factor A transcription factor that binds to a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein (other transcription factors of cofactors) or protein or macromolecular complex. (modified from [GO:0003700]) gene regulatory protein transcription factor activity GO:0003700 transcription factor activity The function of binding to 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:0003700] transcription factor binding site of DNA A region on DNA that specifically forms a chemical bond with one or more transcription factors. transcription factor complex 2 Any protein group composed of two or more transcription factors. transcription initiation GO:0006352 transcription initiation Processes involved in the assembly of the RNA polymerase complex at the promoter region of a DNA template resulting in the subsequent synthesis of RNA from that promoter. [GO:0006352] transcription initiation complex The completed assembly of transcription factors and RNA polymerase binding to the promoter. transcription of gene GO:0006350 transcription The synthesis of either RNA on a template of DNA or DNA on a template of RNA. [GO:0006350] transcription of operon The synthesis of RNA on a DNA template of operon. transcription of regulon genes The synthesis of RNA on the template of regulon genes. transcription of stimulon genes The synthesis of RNA on the template of stimulon genes. transcription RNA-dependent GO:0006410 transcription RNA-dependent The synthesis of DNA on a template of RNA. [GO:0006410] transcription regulator Protein that has transcription regulator activity. transcription regulator activity GO:0030528 transcription regulator activity Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor. [GO:0030528] transcription repressor Any transcription regulator that prevents or downregulates transcription. transcription inhibitor transcription repressor activity Any transcription regulator activity that prevents or downregulates transcription. [GO:0016564] GO:0016564 transcription repressor activity transcription termination GO:0006353 transcription termination The process by which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA. [GO:0006353] transcriptional attenuation Regulation of transcription through variation in where transcription termination occurs. [GO:0031555] GO:0031555 transcriptional attenuation translation GO:0006412 translation The chemical reactions and pathways resulting in the formation of a protein. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein. [GO:0006412] translation elongation GO:0006414 translational elongation The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. [GO:0006414] The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. [GO:0006414] GO:0006414 translational elongation translation factor Any of a group of proteins involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome. translation initiation GO:0006413 translational initiation The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA. [GO:0006413] translation initiation complex GO:0003743 translation initiation factor activity; IMR:0000901 translation initiation factor The protein complex that initiates ribosome-mediated translation of mRNA into a polypeptide (modified from [GO:0003743]). translation regulator Any substance involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome (modified from [GO:0045182]). GO:0045182 translation regulator activity translation termination GO:0006415 translational termination The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). [GO:0006415] translational attenuation Translational attenuation is a regulatory mechanism analogous to ribosome-mediated transcriptional attenuation. The system requires the presence of a short ORF, called a leader peptide, encoded in the mRNA upstream of the ribosome-binding site and start codon of the gene whose translation is to be regulated. Certain conditions, such as presence of the antibiotic tetracycline in bacteria or amino acid starvation, may cause slowing or stalling of the ribosome translating the leader peptide. The stalled ribosome masks a region of the mRNA and affects which of two alternative mRNA folded structures will form, therefore controlling whether or not a ribosome will bind and initiate translation of the downstream gene. Translational attenuation is analogous to ribosome-mediated transcriptional attenuation, in which mRNA remodeling caused by ribosome stalling regulates transcriptional termination rather than translational initiation. [GO:0031555] GO:0031555 translational attenuation translational frameshifting GO:0006452 translational frameshifting A mechanism whereby different proteins may result from a single mRNA molecule, due to a change in the parsing of three nucleotides per codon relative to an initiating AUG codon. [GO:0006452] translational readthrough GO:0006451 translational readthrough The continuation of translation beyond a stop codon by the use of a special tRNA that recognizes the UAG and UGA codons as modified amino acids, rather than as termination codons. [GO:0006451] transport GO:0006810 transport The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.[GO:0006810] transposition Any process involved in mediating the movement of discrete segments of DNA between nonhomolgous sites. [GO:0032196] GO:0032196 transposition tryptophan cluster A region comprising several tryptophan residues with a spacing of 12-21 amino acid residues; the subclass of myb-type DNA-binding domains typically exhibit a spacing of 19-21 amino acid residues. All IRF family members, except IRF-1 and IRF-2, contain conserved IAD, IRF association domain that is responsible for protein-protein interactions with other IRF family members or with Ets factor PU.1 and/or bHLH factor E47. (modified from [TRANSFAC:C0022]) tryptophan cluster transcription factor A transcription factor containing tryptophan cluster. two-component regulatory system System of proteins and other molecular entities responding to environmental changes. Characterized usually by first a sensor kinase in the cell membrane that phosphorylates itself in response to a signal and, second, a response regulator to which the phosphoryl group is transferred. The responder is typically a DNA-binding protein that regulates transcription. Several of these systems are quite complex, involving many proteins in a signaling cascade or contributing to several responses simultaneously. They are involved in a variety processes such as chemotaxis, osmoregulation, magnesium transport, pH tolerance, sporulation, or response of virulent species to host cell's environments. phospho-relay system phosphorelay system two-component sensory transduction system two-component signal transduction system two-component system unpacked DNA The DNA that is unpacked from the loosen chromatin and hence get easy access to various enzymes like DNA polymerase or RNA polymerase in replication or transcription of gene. upstream regulatory sequence A sequence located in the upstream region of a gene that controls the rate or manner in which the gene is expressed. virus A submicroscopic organism that contains genetic information but cannot reproduce itself. To replicate, it must invade another cell and use parts of that cell's reproductive machinery. [http://www.siebelinstitute.com/brewterms/V.html] NCBI Taxonomy ID: 10239 Viruses vitamin CHEBI:33229 vitamin IMR:0001656 vitamin Organic substances that are required in small amounts for maintenance and growth, but which cannot be manufactured by the human body. [MeSH:D014815] WRKY domain The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural stud! WRKY transcription factor A transcription factor containing WRKY domain. X chromosome GO:0000805 X chromosome The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males. [GO:0000805] Y chromosome The sex chromosome present in males of species in which the male is the heterogametic sex; generally, the sex chromosome that pairs with the X chromosome in the heterogametic sex. The Y chromosome is absent from the cells of females and present in one copy in the somatic cells of males. [GO:0000806] GO:0000806 Y chromosome zinc-coordinating domain A domain that coordinates one or more zinc atoms. The zinc-coordinating domains show versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein) and are stable scaffolds that have evolved specialized functions. zinc coordinating domain transcription factor A transcription factor containing zinc coordinating domain. 3' polyadenylation GO:0006378 mRNA polyadenylation The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript. [GO:0006378] polyadenylation at the 3' end 5' capping GO:0009452 RNA capping The sequence of enzymatic reactions by which the 5' cap structure, an inverted 7-methylguanosine linked via a 5'-5' triphosphate bridge (m7G(5')ppp(5')X) to the first transcribed residue, is added to a nascent RNA polymerase II transcript. [GO:0009452] b HLH The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways. bHLH proteins include MyoD, SREBPs (sterol regulatory element binding proteins), and yeast Pho4 (phosphatase system). In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf. [InterPro: IPR011598] bHLH transcription factor A transcription factor containing bHLH domain b HSH A helix-span-helix domain in the C-terminal region of activator protein-2 (AP-2) transcription factors, which mediates dimerisation and site-specific DNA binding. (modified from [InterPro:IPR013854]) bHSH transcription factor A transcription factor containing bHSH domain b ZIP A domain containing a basic region followed by a leucine zipper region, which is required for protein protein interaction. bZIP transcription factor A transcription factor that contains a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region for protein dimerization. p 53 like This domain is found in a number of transcription factors, including p53, NFATC, TonEBP, STAT-1, and NFkappaB, where it is responsible for DNA-binding. These transcription factors play diverse roles in the regulation of cellular functions: the p53 tumour suppressor upregulates the expression of genes involved in cell cycle arrest and apoptosis; NFATC regulates the production of effector proteins involved in coordinating the immune response; TonEBP regulates gene expression induced by osmotic stress and helps regulate intracellular volume during cell growth; STAT-1 plays an important role in B lymphocyte growth and function; and NFkappaB is involved in the inflammatory response. The DNA-binding domain acts to clamp, or in the case of TonEBP, encircle the DNA target in order to stabilize the protein-DNA complex. Protein interactions may also serve to stabilize the protein-DNA complex, for example in the STAT-1 dimer the SH2 (Src homology 2) domain in each monomer is coup! p53-like transcription factor A transcription factor containing p53-like domain. tRNA SO:0000253 tRNA Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position. [SO:0000253, http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732] DIRECTED-BINARY-RELATION PAL-CONSTRAINT en negative