Bioinformatics Advance Access published online on December 20, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl633
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1 Équipe de Statistique Appliquée, École Supérieure de Physique et de Chimie Industrielles (ESPCI), 10 rue Vauquelin, 75005 Paris, France
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-square, 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-square test being equivalent. We discuss the appropriateness of one- and two-sided p-values, as well as some discreteness and conservatism issues.
Received June 20, 2006
Revised December 11, 2006
Accepted December 11, 2006
Review
Enrichment or depletion of a GO category within a class of genes: which test?
Isabelle Rivals 1 *, Léon Personnaz 1, Lieng Taing 2, and Marie-Claude Potier 2
2 Laboratoire de Neurobiologie et Diversité Cellulaire, École Supérieure de Physique et de Chimie Industrielles (ESPCI), 10 rue Vauquelin, 75005 Paris, France
Abstract
Associate Editor: Jonathan Wren
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