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All About the CGAP GO Browser

Overview

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

The GO Browser

1. Symbols

   Symbol	Description
   	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.
   	The term has descendants, not currently displayed, and is "a part of" its parent. Selecting the "+" will cause the descendents to be displayed.
   	The term has descendents that are currently displayed, and is "a kind of" its parent. Selecting the "-" will cause the descendents to become hidden.
   	The term has descendents that are currently displayed, and is "a part of" its parent. Selecting the "-" will cause the descendents to become hidden.
   	The term has no descendents (i.e. it is a "terminal" term) and has the relation "is a kind of" to its parent.
   	The term has no descendents and has the relation "is a part of" to its parent.

   
   

2. 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.
   
   
3. 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.

   • 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.