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All About the CGAP GO Browser
The Gene Ontology (GO) Consortium
is developing a dynamic controlled vocabulary that can be used to annotate all eukaryotic
genes.
GOA (GO Annotation@EBI) is a project run by the
European Bioinformatics Institute
that aims to provide assignments of gene products to the Gene Ontology (GO) resource.
CGAP has designed the Gene Ontology (GO) Browser to allow you to look through
this hierarchical vocabulary, and to find the known human and mouse genes assigned to each term.
By clicking on a hyperlinked number in parenthesis
after a term, a list of the genes within this section is found, with links to the
individual Gene Info pages.
The CGAP GO Browser is updated every few months.
Organization of the GO Vocabulary |
The GO vocabulary has a hierarchical structure that permits a range of
detail from high-level, broadly descriptive terms to very low-level, highly
specific terms. The complete vocabulary is structured into three broad categories,
reflecting the biological roles of genes:
- Molecular Function - tasks performed by individual gene products
- Biological Process - broad biological goals accomplished by ordered assemblies of molecular functions
- Cellular Component - subcellular structures, locations, and macromolecular complexes
- Symbols
Symbol | Description |
![plus: The term has descendents (i.e., it is a "non-terminal" term), not currently displayed, and is "a kind of" its parent. Selecting the "+" will cause the descendents to be displayed.](images/plus.gif) | The term has descendents (i.e., it is a "non-terminal" term), not currently displayed, and is "a kind of" its parent. Selecting the "+" will cause the descendents to be displayed. |
![plusps: The term has descendants, not currently displayed, and is "a part of" its parent. Selecting the "+" will cause the descendents to be displayed.](images/plusps.gif) |
The term has descendants, not currently displayed, and
is "a part of" its parent. Selecting the "+" will cause the descendents
to be displayed. |
![minus: The term has descendents that are currently displayed, and is "a kind of" its parent. Selecting the "-" will cause the descendents to become hidden.](images/minus.gif) | The term has descendents
that are currently displayed, and is "a kind of" its parent. Selecting the "-" will cause the descendents to become
hidden. |
![minusps: The term has descendents that are currently displayed, and is "a part of" its parent. Selecting the "-" will cause the descendents to become hidden.](images/minusps.gif) | The term has descendents
that are currently displayed, and is "a part of" its parent. Selecting the "-" will cause the descendents to become
hidden. |
![isa: The term has no descendents (i.e. it is a "terminal" term) and has the relation "is a kind of" to its parent.](images/isa.gif) | The term has no descendents (i.e. it is a "terminal" term) and
has the relation "is a kind of" to its parent. |
![partof: The term has no descendents and has the relation "is a part of" to its parent.](images/partof.gif) | The term has no
descendents and has
the relation "is a part of" to its parent. |
- Color of Text and Numbers
- A term in green text is the most recently selected term.
- A term may be followed by bracketed numbers indicating the number of human ["Hs:"]
or mouse ["Mm:"] genes that have been classified with that
term.
- Genes
- Selecting either the number in parenthesis of human or mouse genes will
cause a list of these genes to be displayed in the main CGAP window.
- A gene may belong to more than one classification, e.g., TNF (tumor necrosis factor)
can be found under the following 13 terms:
apoptosis,
anti-apoptosis,
cell-cell signalling,
inflammatory response,
leukocyte cell adhesion,
necrosis,
response to pest/pathogen/parasite,
response to viruses,
response to wounding
signal transduction,
soluble fraction
transcription regulation, and
tumor necrosis factor receptor ligand.
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- Genes can be associated with non-terminal terms ("+" and "-")
and with terminal terms ("I" or "P"). In the GO Browser, the number of genes
shown with a non-terminal term is the sum of (a) the number of genes associated
directly with that non-terminal term, and
(b) the count of all the genes associated with
any descendant
of that non-terminal term.
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