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Bioinformatics Advance Access published online on May 29, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn250
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Ontologizer 2.0 - A Multifunctional Tool for GO Term Enrichment Analysis and Data Exploration

Sebastian Bauer a, Steffen Grossmann b, Martin Vingron b and Peter N. Robinson a,*

aInstitute of Medical Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, bMax-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany

*To whom correspondence should be addressed. Dr. Peter N. Robinson, E-mail: sebastian.bauer{at}charite.de, peter.robinson{at}charite.de


  Abstract

Summary: The Ontologizer is a Java application that can be used to perform statistical analysis for overrepresentation of Gene-Ontology (GO) terms in sets of genes or proteins derived from an experiment. The Ontologizer implements the standard approach to statistical analysis based on the one-sided Fisher's exact test, the novel parent-child method (Grossmann et al., 2007), as well as topologybased algorithms (Alexa el al., 2006). A number of multiple-testing correction procedures are provided. The Ontologizer allows users to visualize data as a graph including all significantly overrepresented GO terms and to explore the data by linking GO terms to all genes/proteins annotated to the term and by linking individual terms to child terms.

Availability: The Ontologizer application is available under the terms of the GNU GPL. It can be started as a WebStart application from the project homepage, where source code is also provided:http://compbio.charite.de/ontologizer.

Requirements: Ontologizer requires a Java SE 5.0 compliant Java runtime engine and GraphViz for the optional graph visualization tool.

Contact: sebastian.bauer{at}charite.de, peter.robinson{at}charite.de

Associate Editor: Prof. Dmitrij Frishman

Received on January 30, 2008; revised on April 11, 2008; accepted on May 27, 2008

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