Using GOstats to Test Gene Lists for GO Term Association.

S. Falcon,R. Gentleman

Bioinformatics（2006）CCF BSCI 3区SCI 2区

Fred Hutchinson Canc Res Ctr

被引用2300|浏览9

摘要

MOTIVATION:Functional analyses based on the association of Gene Ontology (GO) terms to genes in a selected gene list are useful bioinformatic tools and the GOstats package has been widely used to perform such computations. In this paper we report significant improvements and extensions such as support for conditional testing.RESULTS:We discuss the capabilities of GOstats, a Bioconductor package written in R, that allows users to test GO terms for over or under-representation using either a classical hypergeometric test or a conditional hypergeometric that uses the relationships among GO terms to decorrelate the results.AVAILABILITY:GOstats is available as an R package from the Bioconductor project: http://bioconductor.org

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关键词

Bioconductor package,GOstats package,R package,Bioconductor project,classical hypergeometric test,conditional hypergeometric,conditional testing,Gene Ontology,functional analysis,selected gene list,term association