This help document answers questions about the top, middle, and bottom sections of the Gene Ontology Classifications report and describes the fields in the linked GO Annotations in Tabular Form page. Access to this report is from an MGI Gene Detail page or from a reference's Curated Data Functional annotations (GO) link.
- Symbol of the mouse genetic marker, linked to its detail page
- Name of the gene/marker/genome feature
- ID: MGI accession identifier.
- GO Annotations Summary Text - details about the gene/marker/genome feature with links to related MGI gene, sequence, Gene Ontology Browser Term detail, and/or reference pages which place this feature in a variety of contexts.
- Tabular View - A link to this data in table format. GO evidence code abbreviations are defined at the bottom of this page.
- GO Graph - A link to GO Annotations in graphical format, for visualizing this data.
- GO annotation of the gene record in tabular form, sorted first by category (molecular function, cellular component, biological process), second by classification term, and finally by evidence code.
- Links to the Gene Ontology Browser term detail pages (from the Classification Term column). If a gene record is annotated with multiple terms, browse the GO vocabulary from this section to narrow the selection.
- Links from Ref(s) column to MGI Reference Detail about the annotation
- Link (back) to summary text in middle section
- Link to GO Graph, for visualizing this the data
- The ability to Export the table in Text (.txt) or Spreadsheet (.xlsx) formats.
Field Descriptions: GO Annotations in Tabular Form
Depending upon how you accessed this page, the following fields may be present. You can Filter the results by Aspect, Category and Evidence Code and Export the table in Text (.txt) or Spreadsheet (.xlsx) formats.
||Isoforms of the protein. These may be different proteins of a gene derived by alternative splicing, alternative start site, modified protein forms, functional protein fragments and combinations of the above.|
||One of three major groups into which all GO terms are organized: Molecular Function, Cellular Component, Biological Process.|
||The categories are from a subset of the Gene Ontologies (a "GO slim") and each category provides an overview of a section of the ontology.|
||Specific GO term used to describe the given gene, linked to the GO Browser.
For more details, see the Gene Ontology Annotation Conventions notes on qualifiers.
- Not can appear before a term from any of the three ontologies. Curators use it to note explicitly that the gene product is not associated with the GO term.
- colocalizes with appears only with cellular component terms. Curators use it:
As an example, colocalizes with would appear when light microscope evidence localizes a gene product to i.e., a cellular complex, but there is no evidence that the gene product is a part of that complex.
- to annotate gene products transiently or peripherally associated with an organelle or complex to the relevant cellular component term;
- in cases where the resolution of an assay is not accurate enough to say that the gene product is a bona fide component member.
- contributes to appears only with molecular function terms. Curators use this annotation when a gene product contributes to a molecular function, but is not in itself sufficient for the function. Annotating individual gene products according to attributes of a complex is especially useful for molecular function annotations in cases where a complex has an activity, but not all of the individual subunits do. As an example, there may be a known catalytic subunit and one or more additional subunits, or the activity may only be present when the complex is assembled.
- Not colocalizes with/Not contributes to implies that a gene product is expected to colocalize with/contribute to a cellular component/molecular function but is found not to do so by one of the GO evidence criteria.
||Adds value to the classification term by detailing the conditions or refining the tissue used in the experiment.|
|Evidence||Criteria that justify the annotation. GO evidence codes appearing on the MGI Gene Ontology Classifications and how they are used are listed below. For additional details, see the Guide to GO Evidence Codes at the Gene Ontology web site.
|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|
|IEA||Inferred from Electronic Annotation|
|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 Or Structural Similarity|
|NAS||Non-traceable Author Statement|
|ND||No biological Data available|
|RCA||Inferred from Reviewed Computational Analysis|
|TAS||Traceable Author Statement|
|Inferred From||GenBank, UniProt, RefSeq, or MGI Gene or Allele Accession ID.|
|Reference(s)||J number (every reference stored in MGI has a number with the format J:nnnnnn) of the supporting reference for the classification, linked to a References Query Results -- Details page. Note: If there are more than 3 references, that numeral replaces the J number, and the link goes to the References Query Results -- Summary page. |