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SAGE Publications, Statistical Methods in Medical Research, 6(18), p. 565-575

DOI: 10.1177/0962280209351908

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Gene Set Enrichment Analysis Made Simple

Journal article published in 2009 by Rafael A. Irizarry, Chi Wang, Chi Wang, Yun Zhou, Terence P. Speed
This paper is available in a repository.
This paper is available in a repository.

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Data provided by SHERPA/RoMEO

Abstract

Among the many applications of microarray technology, one of the most popular is the identification of genes that are differentially expressed in two conditions. A common statistical approach is to quantify the interest of each gene with a p-value, adjust these p-values for multiple comparisons, chose an appropriate cut-off, and create a list of candidate genes. This approach has been criticized for ignoring biological knowledge regarding how genes work together. Recently a series of methods, that do incorporate biological knowledge, have been proposed. However, many of these methods seem overly complicated. Furthermore, the most popular method, Gene Set Enrichment Analysis (GSEA), is based on a statistical test known for its lack of sensitivity. In this paper we compare the performance of a simple alternative to GSEA. We find that this simple solution clearly outperforms GSEA. We demonstrate this with eight different microarray datasets.