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Bioinformatics Advance Access originally published online on May 29, 2008
Bioinformatics 2008 24(14):1650-1651; 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 1,*, Steffen Grossmann 2, Martin Vingron 2 and Peter N. Robinson 1,*

1Institute of Medical Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and 2Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany

*To whom correspondence should be addressed.


  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, as well as topology-based algorithms. 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: Dmitrij Frishman

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

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