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Functional Annotation using the Gene Ontology (GO)
MGI's GO project provides functional annotations for mouse gene products using the Gene Ontology.
Access Data
Browse the Gene Ontology and mouse annotations in MGI.
GO Browser
Search for genes using GO terms and other gene attributes.
Genes & Markers Query
Access GO annotations for genes associated with OMIM.
Comparison Graphs by OMIM gene or disease ID
Obtain sets of MGI IDs for use in GO tools.
Batch Query
Use GO annotations to discover what your gene set may have in common:
MGI GO Term Finder - Analyze functional annotations
GO Chart Tool - Build GO charts to present GO functional data
Access GO annotations for genes from the GO Consortium reference genome project.
Reference Genome Graphs
FAQs
How do I...
.. download all mouse GO annotations? FAQ
.. find all GO annotations for a specific mouse gene? FAQ
.. find all mouse genes with shared annotation to a GO term? FAQ
.. find shared function for a list of specific mouse genes? FAQ
.. view annotations for mouse/human/rat ortholog sets? FAQ
.. obtain FASTA sequence files for mouse genes with GO annotations in common? FAQ
.. find and download the list of all GO Consortium Reference Genome Project mouse genes? FAQ
More FAQs
Functional Annotations (GO) Data Includes
06 Nov 2009
18,140
Mouse genes with GO annotations
8,305
Mouse genes with experimentally-derived GO annotations
1,886
Mouse genes with comprehensive GO annotations
144,197
GO annotations total
13,133
Unique references used for GO annotations
832
Mouse genes selected for GO Reference Genome Project
More...
Gene Ontology at MGI News
March 26, 2009
  • An article by Mary Dolan and Judith Blake describes using ontology visualization to facilitate access to knowledge about human disease genes. See Applied Ontology 2009; 4(1):35-49.
  • Alex Diehl and David Hill among the authors of a paper on muscle research and gene ontology. See PubMed
  • A new evidence code, EXP, is available for groups contributing high-quality manually-curated GO annotations from published experimental results, but who are unable to apply a specific experimental evidence code to each annotation.
  • On April 1, 2008, GO introduced three new evidence codes:
    • ISO - Inferred from sequence orthology
    • ISA - Inferred from sequence alignment
    • ISM - Inferred from sequence model
  • On March 25, 2008, the Gene Ontology Consortium introduced three new relationship types — regulates, negatively_regulates and positively_regulates — into the Biological Process ontology. Until now, regulatory processes have been represented as part_of the processes they regulate. These part_of relationships have been replaced with the new "regulates" relationship types. http://www.geneontology.org/GO.doc.shtml#topology
  • GO curators at MGI are active participants in ontology development projects including revisions of the subtrees for "blood pressure regulation" and "muscle development." If you would like to participate in the community annotation of gene products involved in these processes, please visit the community annotation wikis.
MGI-Mouse Functional Annotation using the Gene Ontology (GO): About GO - Functional Annotation using the Gene Ontology (GO): About
The Mouse Genome Informatics group is a founding member of the Gene Ontology Consortium (www.geneontology.org). MGI fully incorporates the GO in the database and provides a GO browser.

What is a Gene Ontology annotation?

Gene Ontology annotation is a manually or automatically assigned text file containing the following information:

  • Gene name, symbol
  • Gene Ontology term
  • Published reference
  • Evidence code
  • Date of the annotation
  • Optional information (Qualifiers such as "NOT", "contributes_to", "colocalizes_with"; Notes with both free text and controlled vocabulary information)

What is manual annotation?

Scientific curators use published literature to assign GO terms based on evidence codes, which support the annotation.

What are evidence codes?

MGI uses the following evidence codes:

  • Manually assigned:
    • EXP - Inferred from experiment
    • IDA - Inferred from direct assay
    • IMP - Inferred from mutant phenotype
    • IPI - Inferred from physical Interaction
    • IGI - Inferred from genetic interaction
    • ISS - Inferred from sequence and structural similarity
    • ISO - Inferred from sequence orthology
    • ISA - Inferred from sequence alignment
    • ISM - Inferred from sequence model
    • IC - Inferred by curator
    • ND - Not determined
  • Automatically assigned:
    • IEA - Inferred from electronic annotation
Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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Send questions and comments to User Support. 		last database update
11/06/2009
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