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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
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 homolog 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
08 Oct 2014
24,317
Mouse protein-coding genes with GO annotations
11,151
Mouse protein-coding genes with experimentally-derived in mouse GO annotations
26,048
Mouse genes with 'complete' annotations based on current literature review
294,347
GO annotations total
22,251
Unique references used for GO annotations
987
Mouse genes selected for GO Reference Genome Project
More...
Gene Ontology at MGI News
March, 2014
  • Karen Christie presented a poster at the 2014 Keystone Symposia on Cilia, Development and Human Disease:
    Karen R. Christie and Judith A. Blake. Comprehensive Gene Ontology annotation of ciliary genes in the laboratory mouse.
  • Li Ni presented a poster at the 2013 International Mammalian Genome Society meeting:
    Li Ni, Mary E. Dolan, Judith A. Blake. Assessment of comparative functional annotation propagation in mouse.
    Abstract: Annotations that have been curated from the literature by domain experts are considered the most valuable component of this effort, but manual curation is very labor intensive compared with semi-automated methods for assignment of functional annotation. Since genes that share close evolutionary relationships are likely to function in similar ways, many applications leverage phylogenetic relationships to propagate functional annotation from related genes. MGI's use of N:M homology sets has led to the refinement of rules for semi-automated annotation propagation. In this work we assess the quantity and quality of various methods of automated propagation of functional annotations.
  • MGI has long provided one-to-one orthologous mammalian relationships and used these to infer the function of mouse genes from experimentally determined knowledge about human and rat genes. Recently, MGI implemented a "many-to-many" homology paradigm to better reflect current understanding about the relationships between genes of these three organisms. Although one-to-one orthology assertions between mouse/human/rat genes still holds for 90% of protein-coding genes, MGI can now more clearly represent cases where phylogenetic analysis shows multiple mouse, human, or rat genes in the same orthology class.
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
    • IAS - Inferred from ancestral sequence
    • IBA - Inferred from biological aspect of ancestor
    • IBD - Inferred from biological aspect of descendant
    • IC - Inferred by curator
    • IDA - Inferred from direct assay
    • IGI - Inferred from genetic interaction
    • IKR - Inferred from key residues
    • IMP - Inferred from mutant phenotype
    • IMR - Inferred from missing residues
    • IPI - Inferred from physical Interaction
    • IRD - Inferred from rapid divergence
    • ISA - Inferred from sequence alignment
    • ISM - Inferred from sequence model
    • ISO - Inferred from sequence orthology
    • ISS - Inferred from sequence and structural similarity
    • 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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last database update
10/08/2014
MGI 5.20
The Jackson Laboratory