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

作     者：Rivals, Isabelle Personnaz, Leon Taing, Lieng Potier, Marie-Claude 

作者机构：Ecole Super Phys & Chim Ind Ville Paris Equipe Stat Appl F-75005 Paris France Ecole Super Phys & Chim Ind Ville Paris Lab Neurobiol & Divers Cellulaire F-75005 Paris France 

出 版 物：《BIOINFORMATICS》 (生物信息学)

年 卷 期：2007年第23卷第4期

页      面：401-407页

核心收录：

学科分类：0710[理学-生物学] 08[工学] 0714[理学-统计学（可授理学、经济学学位）] 0836[工学-生物工程] 0812[工学-计算机科学与技术（可授工学、理学学位）] 

主　　题：MICROARRAY DATA EXPRESSION DATA ONTOLOGY TERMS TOOL 

摘      要：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:***@*** Supplementary information: Supplementary data are available at Bioinformatics online.