Using GOstats to test gene lists for GO term association

Bioinformatics - Tập 23 Số 2 - Trang 257-258 - 2007
Seth Falcon1, Robert Gentleman1
1Fred Hutchison Cancer Research Center, Program Computational Biology,1100 Fairview Avenue North   P. O. Box 19024, Seattle, WA 98109, USA

Tóm tắt

AbstractMotivation: 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:  [email protected]

Từ khóa


Tài liệu tham khảo

Alexa, 2006, Improved scoring of functional groups from gene expression data by decorrelating GO graph structure, Bioinformatics, 22, 1600, 10.1093/bioinformatics/btl140

Chiaretti, 2004, Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival, Blood, 103, 2771, 10.1182/blood-2003-09-3243

GO Consortium, 2000, Gene Ontology: tool for the unification of biology, Nat. Genetics, 25, 25, 10.1038/75556

Thông tin
Thông tin xuất bản

Bioinformatics

Tập 23 Số 2

257-258

Thông tin tác giả