Using GOstats to test gene lists for GO term association
Using GOstats to test gene lists for GO term association
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DOI：
10.1093/bioinformatics/btl567
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发表时间：
2007-01-15
期刊：
影响因子：
5.8
通讯作者：
Gentleman, R.
中科院分区：
文献类型：
--
作者：
Falcon, S.;Gentleman, R.
动机：基于基因本体（GO）术语与选定基因列表中基因的关联的功能分析是有用的生物信息学工具，GOstats包已被广泛用于执行此类计算。在本文中，我们报告了重大的改进和扩展，例如对条件测试的支持。结果：我们讨论了GOstats的功能，GOstats是一个用R语言编写的Bioconductor包，它允许用户使用经典超几何测试或条件超几何测试来测试GO术语的过度或不足表示，该测试使用GO术语之间的关系来解除结果的相关性。
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.