We wish to acknowledge the developers of the MeSH Browser for their user interface design. Please reference: Chang HF, Nelson SJ. 1999. Presenting MeSH Data Over the Web. JAMIA Symposium Supplement: 1037.
This Gene Ontology (GO) Browser help document answers the following questions:
The GO vocabularies have a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. The range is useful for annotating genes and searching for gene information using these terms as search criteria. You can either browse or search the vocabularies from the Browser main page.Top
To browse the GO, click on one of the three broad categories that reflect the biological roles of genes.
|Molecular Function||GO:0003674||Tasks performed by individual gene products.||Transcription factor; DNA helicase|
|Cellular Component||GO:0005575||Subcellular structures, locations, and macromolecular complexes||Nucleus; telomere; origin recognition complex|
|Biological Process||GO:0008150||Broad biological goals accomplished by ordered assemblies of molecular functions||Mitosis; purine metabolism|
The Gene Ontology Browser Term Detail page contains the following information. The item of interest appears in red. Click the blue label indicating the number of genes and annotations (e.g. 45 genes, 55 annotations) to see the Gene Ontology Annotations Query Results.
|GO term, GO id, Definition, Synonym, Comments, Number of paths to term||Selected GO term, unique identifier for the term, definition of the term, synonyms for the term if available, any curatorial comments, and the number of paths to the term. The comments area may contain information such as that a GO term is obsolete, reasons for obsoleting, and suggestions for alternate annotation choices. Note: Click on any detail term to see its associated structures or synonyms.|
|Links||A list of all paths to the term. Click on the desired link to bring up a detail for that term.|
|"Is-a" Relationship||Indicates that the term is an instance or type of the more general term above it in the tree. For example, metabolism is a type of cell growth and maintenance.|
|"Part-of" Relationship||Indicates that the term is a component of the more general term above in the tree. For example, cell cycle arrest is a part of the cell cycle process.|
|"Regulates" Relationship||Indicates that the term modulates the frequency, rate, or extent of the term above it in the tree.|
|"Regulates upward" Relationship||Indicates that the term activates or increases the frequency, rate, or extent of the term above it in the tree.|
|"Regulates downward" Relationship||Indicates that the term stops, prevents, or reduces the frequency, rate, or extent of the term above it in the tree.|
|+||A plus sign (+) following a term indicates that the term has children. Click on the term to see the additional paths.|
|Unique identifier||Name of the ontology selected, followed by the a unique identifier. There is one identifier for each GO term in the GO. This means that no matter how many times the term appears, the ID is always the same. This is also true if the term changes. For example, if cell growth and maintenance becomes simply cell growth, the GO identifier does not change.|
|# genes, #annotations||Number of markers annotated to the term and its descendants, followed by the number of annotations to each term and its decedents. Click this label to see the Gene Ontology Annotations Query Results.|
If you enter the GO identifier, the Browser searches a vocabulary by ID and returns only an exact match on the ID string. For example, to see all of the GO terms for molecular function, enter GO:0003674. The GO Browser - Query Results lists all matches found.Top
The Gene Ontology Browser - Query Results lists all matches found per ontology (molecular function, cellular component, biological process). Locate the item of interest and click the desired term from the list to see Term Details.Top
|Symbol, Name | Chr | Category | Annotated Term | Evidence | Refs|
|Symbol, Name||The symbol for the mouse genetic marker (linked to its MGI gene detail ), followed by the name for this marker.|
|Chr||The chromosome number (or letter) location of the marker.|
|Category||All GO terms are organized into three major categories; the letter indicates the category for each annotation:
|Specific GO term used to describe the given gene, linked to its Gene Ontology Term Detail (see How do I interpret Term Details? for details.) Note: Annotated Terms may be preceded by qualifiers:
|Evidence||Criteria that justify the annotation. The most common GO evidence codes appear in the table below.
For a complete list and the most current information, see Guide to GO Evidence Codes at the Gene Ontology web site.
|Ref(s)||J number (every reference stored in MGI has a number with the format J:nnnn) of the supporting reference for the classification, linked to References Query Results -- Details. Note: If there are more than three references, that numeral replaces the J number, and the link goes to Reference Query Results.|