Thu, 21 Aug 2008 15:13:49 BST CiteULike: capitall Taing http://www.citeulike.org/user/capitall/author/Taing CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/capitall/article/1056288 <i>Bioinformatics (20 December 2006)</i><br /><br />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. Enrichment or depletion of a GO category within a class of genes: which test? Isabelle Rivals Léon Personnaz Lieng Taing Marie-Claude Potier doi:10.1093/bioinformatics/btl633 Bioinformatics (20 December 2006) 2007-01-20T19:50:10-00:00 2006 Bioinformatics 1460-2059 bioinformatics ease mev nested-ease