Using GOstats to test gene lists for GO term association
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Open Access
- 10 November 2006
- journal article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 23 (2) , 257-258
- https://doi.org/10.1093/bioinformatics/btl567
Abstract
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:Contact: sfalcon@fhcrc.orgKeywords
This publication has 3 references indexed in Scilit:
- Improved scoring of functional groups from gene expression data by decorrelating GO graph structureBioinformatics, 2006
- Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survivalBlood, 2004
- Gene Ontology: tool for the unification of biologyNature Genetics, 2000