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

Isabelle Rivals (1) , Léon Personnaz (1) , Lieng Taing (2) , Potier Marie-Claude (2)

1 ESA - Equipe de Statistique Appliquée (UMRS 1158)
2 Laboratoire de Neurobiologie et de Diversité Cellulaire

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 prob-lem 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, χ2, equality of two probabilities, Fisher's exact, and hypergeometric tests. We clarify the relation-ships 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 equal-ity of two probabilities and the χ2 test being equivalent. We discuss the appropriateness of one- and two-sided p-values, as well as some discreteness and conservatism issues.

Keywords: GO category; Fisher's exact test; hypergeometric test; p-value; p-value.

Domains: Methodology [stat.ME]; Quantitative Methods [q-bio.QM]; Bioinformatics [q-bio.QM]

Isabelle Rivals, Léon Personnaz, Lieng Taing, Potier Marie-Claude. Enrichment or depletion of a GO category within a class of genes: which test?. Bioinformatics, 2007, 23 (4), pp.401-407. ⟨10.1093/bioinformatics/btl633⟩. ⟨hal-00801557⟩