Gene set enrichment analysis: Performance evaluation and usage guidelines

Jui-Hung Hung, Tun Hsiang Yang, Zhenjun Hu, Zhiping Weng*, Charles DeLisi

*此作品的通信作者

研究成果: Article同行評審

124 引文 斯高帕斯(Scopus)

摘要

A central goal of biology is understanding and describing the molecular basis of plasticity: the sets of genes that are combinatorially selected by exogenous and endogenous environmental changes, and the relations among the genes. The most viable current approach to this problem consists of determining whether sets of genes are connected by some common theme, e.g. genes from the same pathway are overrepresented among those whose differential expression in response to a perturbation is most pronounced. There are many approaches to this problem, and the results they produce show a fair amount of dispersion, but they all fall within a common framework consisting of a few basic components. We critically review these components, suggest best practices for carrying out each step, and propose a voting method for meeting the challenge of assessing different methods on a large number of experimental data sets in the absence of a gold standard. Published by Oxford University Press 2011.

原文English
文章編號bbr049
頁(從 - 到)281-291
頁數11
期刊Briefings in Bioinformatics
13
發行號3
DOIs
出版狀態Published - 1 五月 2012

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