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GO Slims and GO Term Comparison

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Introduction

GO slims are lists of GO terms that have been selected from the full set of terms available from the Gene Ontology project.
GO slims can be used to generate a focused view of part of the GO or a broad overview of all of the top GO categories. Used alongside annotation data they can be used to see how a set of proteins/genes can be broadly categorized into selection of terms (this method applies the relationships that exist between terms in the ontologies).
You can use GO slims that have been predefined by members of the GO Consortium, that have been imported into QuickGO, or make a new GO slim that more closely meets with your visualization requirements.
Use the tabs on this page to choose the terms to include in your slim, which you can subsequently edit, visualise the relationships between selected terms and finally have the annotations in QuickGO 'mapped' up to your selected set of terms.
A guide to the GO slims maintained by the GO Consortium is available at http://www.geneontology.org/GO.slims.shtml.

Choose Terms

Predefined GO Term sets
The predefined GO slims listed below have been created by groups in the GO Consortium; you can use them directly, or adapt them to your own requirements.
To use the terms from one of these GO slims, click on the button next to its name.
The colour associated with each predefined GO slim can be used to identify slim terms when viewing the ontology in the Ancestor chart view.
Slim name Number of terms Slim colour
goslim_candida 89
goslim_plant 100
goslim_pir 462
goslim_generic 148
goslim_yeast 167
goslim_aspergillus 85
goslim_pombe 44
goslim_metagenomics 119
Add Terms
If you have selected one of the predefined GO slim sets above, you can use the text box below to add additional GO identifiers to create a customised version of the slim.
Alternatively, if you have decided to create an entirely new GO slim, you can just add GO term identifiers into this text box.
Term Basket
You can add terms from your Term Basket to the slim; click on the icon for more details.

Refine Selection

Your selected terms
You can remove a GO term from the set you have chosen by clicking on the button next to it in the list below; to remove all terms in a particular category, click on the button in the category header.
You can add extra terms to your selection by going back to the Choose Terms tab.
Click on in the list below to add a GO term (or category) to the comparison chart, or to remove it.
All Terms
Biological Process Terms
Molecular Function Terms
Cellular Component Terms
Term Comparison
Click on the thumbnail below (or on the Comparison Chart tab) to display a full-sized term comparison chart.

Comparison Chart

Display options
Display
This chart is interactive; you can click on the term boxes and legend for more information.
Key
GO IDs
Term box width
Term box height
Slim colours
Show children
Image size limit (in megapixels)
Note that setting the limit too high may result in images being generated slowly; it may even cause the browser to crash. The maximum limit is 20 megapixels.

Find Annotations

Displaying annotations FIRST to LAST of TOTAL Page size: Additional filters: Bookmarkable link
Database
Gene Product ID
Symbol
Qualifier
GO Identifier
GO Term Name
Aspect
Original GO ID
Original GO Term Name
Evidence
Reference
With
Taxon
Date
Assigned By
Product Form ID
Name
Synonym
Type
Taxon Name
Sequence

Export

Format:

Limit:

Gzip results:

Note:

 Your current filter returns (annotationCount) annotations for (proteinCount) proteins.
You may need to adjust the Limit value above if it is not sufficient.

Display options

Use this filter to ensure that the annotation table display provides the information you require.

Columns that are currently displayed in the annotation table are indicated in the list below by a checked tick box.
You can tailor the annotation table display to your requirements by selecting or deselecting individual columns.

Display columns:
Database
Gene Product ID
Symbol
Qualifier
GO Identifier
GO Term Name
Aspect
Original GO ID
Original GO Term Name
Evidence
Reference
With
Taxon
Date
Assigned By
Product Form ID
Name
Synonym
Type
Taxon Name
Sequence

You can use the options below to choose whether to be shown an annotation set or a protein list.

Show:
Annotations that match the current filter criteria
Proteins with annotations that match the current filter criteria
All annotations to proteins with annotations that match the current filter criteria

ID Mapping

Use this filter to change between different sequence identifier types.
QuickGO's default is to show annotations to UniProtKB (Swiss-Prot and TrEMBL) accession numbers.

Database CodeDatabase Name
UniProtKB Universal Protein Knowledgebase
UniProtKB/Swiss-Prot UniProtKB/Swiss-Prot
UniProtKB/TrEMBL UniProtKB-TrEMBL protein sequence database
CGD Candida Genome Database
dictyBase dictyBase
EcoCyc Encyclopedia of E. coli metabolism
EMBL EMBL Nucleotide Sequence Database
ENSEMBL_GeneID Ensembl database of automatically annotated genomic data
ENSEMBL_ProteinID Ensembl database of automatically annotated genomic data
ENSEMBL_TranscriptID Ensembl database of automatically annotated genomic data
FB FlyBase
GeneDB_Pfalciparum Plasmodium falciparum GeneDB
GeneID NCBI Gene
GR Gramene
HGNC HUGO Gene Nomenclature Committee
MGI Mouse Genome Informatics
MIM Mendelian Inheritance in Man
PomBase PomBase
RefSeq RefSeq
RGD Rat Genome Database
SGD Saccharomyces Genome Database
TAIR The Arabidopsis Information Resource
TIGR_CMR EGAD database at the J. Craig Venter Institute
UniGene UniGene
WB WormBase database of nematode biology
ZFIN Zebrafish Information Network

QuickGO maps between different identifier types by using a combination of mapping files provided by the databases, and using identifier cross-references supplied by UniProtKB.

If more than one identifier type needs to be used to map all required sequences, drag the selected databases to change the order in which identifiers are found.

Filter

Summary
summary
The tabs in this dialog allow you to filter the set of GO annotations that QuickGO displays.
You can apply multiple filtering parameters to restrict the set of annotations to those that match, for example:
  • a list of gene/protein identifiers (ID)
  • gene products from specified taxonomic groups (Taxon)
  • annotations that apply certain Qualifier types
  • those that are supported by a particular Reference or Evidence type
  • those that use a particular source of external annotation data
  • annotations that have been supplied by a particular GO annotation group
Currently selected additional filtering parameters:
Gene Product ID
proteinID
Currently selected additional filtering parameters:
Find annotations for a defined set of gene or protein identifiers:

To restrict the annotations to a set of gene or protein identifiers, enter a list of IDs in the text box below, separated by commas, spaces or newlines. There is no limit on the number of identifers that can be entered into this box.

You can use identifier types other than UniProtKB accessions (for the full range of acceptable ID types, please see the ID Mapping tab on the Annotation Tool Bar). However please note that QuickGO will automatically map the identifiers to UniProtKB accessions, and unless you have additionally selected a specific Identifier Type to be returned in the annotation set, the default behaviour of this tool will be to display the filtered set of annotations with their corresponding UniProtKB accession numbers.

OR select a list of proteins:
BHF-UCL The set of Cardiovascular-associated proteins being prioritised for annotation by the Cardiovascular Gene Ontology Annotation Initiative located at University College London http://www.ucl.ac.uk/cardiovasculargeneontology
KRUK The set of proteins associated with renal processes being prioritised for annotation by the EBI's Renal Gene Ontology Annotation Initiative http://www.ebi.ac.uk/GOA/kidney/index.html
ReferenceGenome The set of human proteins being comprehensively curated by the UniProt-GOA project as part of the GO Consortium's Reference Genome initiative http://www.geneontology.org/GO.refgenome.shtml
Taxon
proteinTaxon
Currently selected additional filtering parameters:
To filter by species/taxonomic group, list taxon identifiers in the text box or select one or more of the pre-defined taxonomic groups below.
9606 Human
10090 Mouse
40674 Mammalia
3398 Magnoliophyta (flowering plants)
2759 Eukaryota
1117 Cyanobacteria

Visit UniProt Taxonomy to find identifiers for other taxonomic groups

Qualifier
qualifier
Currently selected additional filtering parameters:

The Qualifier column in a GO annotation is used for flags that modify the interpretation of an annotation. Allowable values are NOT, contributes_to, and colocalizes_with.

Further details on the usage of the qualifier column can be found here.

contributes_to An individual protein that is part of a complex can be annotated to terms that describe the action of the complex. This qualifier allows us to distinguish individual subunit from complex functions e.g. This protein contributes_to 'ribosome binding' when part of a complex but does not perform this function on its own.
NOT|colocalizes_with NOT|colocalizes_with
NOT|contributes_to NOT|contributes_to
colocalizes_with Proteins that are transiently or peripherally associated with an organelle or complex may be annotated to the relevant cellular component term, using the 'colocalizes_with' qualifier.
NOT Used to make an explicit note that the protein is not associated with the GO term e.g. This protein does NOT have 'kinase activity' as expected, disrupted/missing ATP binding domain.
(none)

GO Identifier
goID
Currently selected additional filtering parameters:
Select the terms that you wish to use

Predefined GO term sets:

Enter a list of GO identifiers (GO:nnnnnnn), separated by space, comma or newline characters:

Select how you want to use the terms that you have chosen
Use these terms as a GO slim
Find annotations to descendants of these terms (annotations will display the original GO terms applied)
Select which relationship an annotated term should have to the terms above:
Default behaviour (is_a, part_of and occurs_in relationships only)
exact match
is_a only
is_a, part_of, occurs_in, regulates, positively_regulates and negatively_regulates
Use all relationships
Custom

Reference
ref
Currently selected additional filtering parameters:

If you want to find annotations that cite one or more specific references, you can enter them in this text box (with or without a database prefix):

Alternatively (or in addition), you can find annotations that cite a particular type of reference by selecting the appropriate check box(es) below:

DOI:* Digital Object Identifier
GO_REF:* Gene Ontology Database references
PMID:* PubMed
Reactome:* Reactome - a curated knowledgebase of biological pathways
GO_REF:0000002 InterPro2GO
GO_REF:0000003 EC2GO
GO_REF:0000019 Ensembl Compara
GO_REF:0000020 HAMAP2GO
GO_REF:0000035 EnsemblPlants/Gramene
GO_REF:0000037 UniProt Keywords2GO (UniProtKB/Swiss-Prot entries)
GO_REF:0000038 UniProt Keywords2GO (UniProtKB/TrEMBL entries)
GO_REF:0000039 UniProt Subcellular Location2GO (UniProtKB/Swiss-Prot entries)
GO_REF:0000040 UniProt Subcellular Location2GO (UniProtKB/TrEMBL entries)
GO_REF:0000041 UniPathway2GO
GO_REF:0000049 EnsemblFungi
Evidence
evidence
Currently selected additional filtering parameters:

A full description of evidence codes and their usage can be found here.

IMP,IGI,IPI,IDA,IEP,EXP Manual Experimental
IMP,IGI,IPI,IDA,IEP,EXP,ISS,TAS,NAS,ND,IC,RCA,IBA,IBD,IKR,IRD,ISA,ISM,ISO,IGC Manual All
IMP Inferred from Mutant Phenotype
IGI Inferred from Genetic Interaction
IPI Inferred from Physical Interaction
IGC Inferred from Genomic Context
ISS Inferred from Sequence or Structural Similarity
IDA Inferred from Direct Assay
IEP Inferred from Expression Pattern
IEA Inferred from Electronic Annotation
TAS Traceable Author Statement
NAS Non-traceable Author Statement
ND No biological Data available
IC Inferred by Curator
RCA Reviewed Computational Annotation
ISA Inferred from Sequence Alignment
EXP Inferred from EXPeriment
IBA Inferred from Biological aspect of Ancestor
IBD Inferred from Biological aspect of Descendant
IKR Inferred from Key Residues
IRD Inferred from Rapid Divergence
ISO Inferred from Sequence Orthology
ISM Inferred from Sequence Model

With
with
Currently selected additional filtering parameters:
AGI_LocusCode:* Arabidopsis Genome Initiative
AspGD:* Aspergillus Genome Database
CGD:* Candida Genome Database
CHEBI:* Chemical Entities of Biological Interest
dictyBase:* dictyBase
EC:* Enzyme Commission
EchoBASE:* EchoBASE post-genomic database for Escherichia coli
ECK:* EcoGene Database of Escherichia coli Sequence and Function
EcoCyc:* Encyclopedia of E. coli metabolism
ECOGENE:* EcoGene Database of Escherichia coli Sequence and Function
EcoliWiki:* EcoliWiki from EcoliHub
EMBL:* EMBL Nucleotide Sequence Database
Ensembl:* Ensembl database of automatically annotated genomic data
EnsemblFungi:* Ensembl Fungi, the Ensembl Genomes database for accessing fungal genome data
EnsemblPlants:* Ensembl Plants, the Ensembl Genomes database for accessing plant genome data
FB:* FlyBase
GB:* GenBank
GenBank:* GenBank
GO:* Gene Ontology Database
GR_PROTEIN:* Gramene
HAMAP:* High-quality Automated and Manual Annotation of microbial Proteomes
InterPro:* InterPro database of protein domains and motifs
JCVI_CMR:* EGAD database at the J. Craig Venter Institute
JCVI_GenProp:* Genome Properties database at the J. Craig Venter Institute
KEGG_LIGAND:* KEGG LIGAND Database
MaizeGDB_Locus:* MaizeGDB
MGI:* Mouse Genome Informatics
NCBI_gi:* NCBI databases
NCBI_GP:* NCBI GenPept
PANTHER:* Protein ANalysis THrough Evolutionary Relationships Classification System
PDB:* Protein Data Bank
Pfam:* Pfam database of protein families
PIR:* Protein Information Resource
PomBase:* PomBase
protein_id:* DDBJ / EMBL-Bank / GenBank
PubChem_Compound:* NCBI PubChem database of chemical structures
PubChem_Substance:* NCBI PubChem database of chemical substances
RefSeq:* RefSeq
RGD:* Rat Genome Database
SGD:* Saccharomyces Genome Database
TAIR:* The Arabidopsis Information Resource
UniPathway:* UniPathway
UniProtKB:* Universal Protein Knowledgebase
UniProtKB-KW:* UniProt Knowledgebase keywords
UniProtKB-SubCell:* UniProt Knowledgebase Subcellular Location vocabulary
WB:* WormBase database of nematode biology
ZFIN:* Zebrafish Information Network

Annotated with (with or without a database prefix):

Aspect
aspect
Currently selected additional filtering parameters:
You can use the check boxes below to limit the scope of the returned annotation set to terms from one or more specific ontologies:
Molecular Function
Biological Process
Cellular Component
Assigned By
from
Currently selected additional filtering parameters:
Select annotation from:
AgBase AgBase resource for functional analysis of agricultural plant and animal gene products
BHF-UCL Cardiovascular Gene Ontology Annotation Initiative
CGD Candida Genome Database
DFLAT Developmental FunctionaL Annotation at Tufts
dictyBase dictyBase
EcoCyc Encyclopedia of E. coli metabolism
EcoliWiki EcoliWiki from EcoliHub
Ensembl Ensembl database of automatically annotated genomic data
EnsemblFungi Ensembl Fungi, the Ensembl Genomes database for accessing fungal genome data
EnsemblPlants/Gramene Ensembl Plants, the Ensembl Genomes database for accessing plant genome data
FlyBase FlyBase
GDB Human Genome Database
GeneDB_Pfalciparum Plasmodium falciparum GeneDB
GOC Gene Ontology Consortium
GR Gramene
HGNC HUGO Gene Nomenclature Committee
HPA Human Protein Atlas tissue profile information
IntAct IntAct protein interaction database
InterPro InterPro database of protein domains and motifs
JCVI J. Craig Venter Institute
LIFEdb LifeDB
MENGO Microbial ENergy processes Gene Ontology Project
MGI Mouse Genome Informatics
MTBBASE Collection and Refinement of Physiological Data on Mycobacterium tuberculosis
NTNU_SB Norwegian University of Science and Technology, Systems Biology team
PAMGO_GAT Genome Annotation Tool (Agrobacterium tumefaciens C58); PAMGO Interest Group
PAMGO_MGG Magnaporthe grisea database
PINC Proteome Inc.
PomBase PomBase
PseudoCAP Pseudomonas Genome Project
Reactome Reactome - a curated knowledgebase of biological pathways
RefGenome GO Reference Genomes
RGD Rat Genome Database
Roslin_Institute Roslin Institute
SGD Saccharomyces Genome Database
TAIR The Arabidopsis Information Resource
TIGR J. Craig Venter Institute
UniProt Universal Protein Knowledgebase
WormBase WormBase database of nematode biology
ZFIN Zebrafish Information Network

Advanced
advanced
Currently selected additional filtering parameters:
Enter query parameters in the text box below. The format of advanced annotation queries is described here.

Select

Categories
Protein
GO ID
Aspect
Evidence
Reference
Taxon
Assigned by
Grouped by
Annotation count
Protein count
Both
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Hostnameves-pg-ce.ebi.ac.uk
Up since13:55 17/9/2013
Stamp2013-10-01-03-06-46
Version46