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Bioinformatics Advance Access originally published online on November 10, 2006
Bioinformatics 2007 23(2):257-258; doi:10.1093/bioinformatics/btl567
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Using GOstats to test gene lists for GO term association

S. Falcon * and R. Gentleman

Fred Hutchison Cancer Research Center, Program Computational Biology,1100 Fairview Avenue North P. O. Box 19024, Seattle, WA 98109, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Functional analyses based on the association of Gene Ontology (GO) terms to genes in a selected gene list are useful bioinformatic tools and the GOstats package has been widely used to perform such computations. In this paper we report significant improvements and extensions such as support for conditional testing.

Results: We discuss the capabilities of GOstats, a Bioconductor package written in R, that allows users to test GO terms for over or under-representation using either a classical hypergeometric test or a conditional hypergeometric that uses the relationships among GO terms to decorrelate the results.

Availability: GOstats is available as an R package from the Bioconductor project: http://bioconductor.org

Contact: sfalcon{at}fhcrc.org

Associate Editor: Trey Ideker

Received on October 16, 2006; accepted on November 3, 2006

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