Gene Ontology Term Analysis

Revision as of 14:08, 11 November 2009 by Smith (talk | contribs) (Ontologizer)

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Overview

The Gene Ontology project describes genes (gene products) using terms from three structured vocabularies: biological process, cellular component and molecular function.

A number of analysis methods in geWorkbench a list of interesting genes, for example, those differentially expressed (t-test), or those which show similarities in expression (Hierarchical Clustering, SOM, ARACNe). The Gene Ontology Enrichment component, also referred to as the "GO Terms" component, allows the genes in such a list to be characterized using their assignments to various categories in the Gene Ontology. It asks, for this list of genes, are any GO categories present at a level higher than expected by chance?


The Gene Ontology (GO Terms) analysis component in geWorkbench is built around the Ontologizer 2.0 software product from Peter Robinson's group at the Charite Medical Institute in Berlin. It provides several methods for enrichment analysis, including Term-for-Term, Parent-Child, and Topology. More information about these methods can be found at the Ontologizer website at http://compbio.charite.de/index.php/ontologizer2.html.


This tutorial is currently being developed and will be complete on November 11, 2009.

Analysis Component GUI

Parameters

Selection

T GO Terms Analysis Parameters Selection.png


Ontologizer

T GO Terms Analysis Parameters Ontologizer.png


T GO Terms Analysis Parameters Ontologizer Enrichment.png


T GO Terms Analysis Parameters Ontologizer MultipleTestingCorrections.png