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BMCBI
2007

Computation of significance scores of unweighted Gene Set Enrichment Analyses

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Computation of significance scores of unweighted Gene Set Enrichment Analyses
Background: Gene Set Enrichment Analysis (GSEA) is a computational method for the statistical evaluation of sorted lists of genes or proteins. Originally GSEA was developed for interpreting microarray gene expression data, but it can be applied to any sorted list of genes. Given the gene list and an arbitrary biological category, GSEA evaluates whether the genes of the considered category are randomly distributed or accumulated on top or bottom of the list. Usually, significance scores (p-values) of GSEA are computed by nonparametric permutation tests, a time consuming procedure that yields only estimates of the p-values. Results: We present a novel dynamic programming algorithm for calculating exact significance values of unweighted Gene Set Enrichment Analyses. Our algorithm avoids typical problems of nonparametric permutation tests, as varying findings in different runs caused by the random sampling procedure. Another advantage of the presented dynamic programming algorithm is its ...
Andreas Keller, Christina Backes, Hans-Peter Lenho
Added 12 Dec 2010
Updated 12 Dec 2010
Type Journal
Year 2007
Where BMCBI
Authors Andreas Keller, Christina Backes, Hans-Peter Lenhof
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