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Bioinformatics Advance Access originally published online on December 20, 2006
Bioinformatics 2007 23(4):401-407; doi:10.1093/bioinformatics/btl633
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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.

Enrichment or depletion of a GO category within a class of genes: which test?

Isabelle Rivals *, Léon Personnaz , Lieng Taing 1 and Marie-Claude Potier 1

Équipe de Statistique Appliquée 10 rue Vauquelin, 75005 Paris, France
1 Laboratoire de Neurobiologie et Diversité Cellulaire, École Supérieure de Physique et de Chimie Industrielles (ESPCI) 10 rue Vauquelin, 75005 Paris, France

*To whom correspondence should be addressed.


  Abstract

Motivation: A number of available program packages determine the significant enrichments and/or depletions of GO categories among a class of genes of interest. Whereas a correct formulation of the problem leads to a single exact null distribution, these GO tools use a large variety of statistical tests whose denominations often do not clarify the underlying P-value computations.

Summary: We review the different formulations of the problem and the tests they lead to: the binomial, {chi}2, equality of two probabilities, Fisher's exact and hypergeometric tests. We clarify the relationships existing between these tests, in particular the equivalence between the hypergeometric test and Fisher's exact test. We recall that the other tests are valid only for large samples, the test of equality of two probabilities and the {chi}2-test being equivalent. We discuss the appropriateness of one- and two-sided P-values, as well as some discreteness and conservatism issues.

Contact: isabelle.rivals{at}espci.fr

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Jonathan Wren

Received on June 20, 2006; revised on December 11, 2006; accepted on December 11, 2006

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