GSEA-P: a desktop application for Gene Set Enrichment Analysis

Abstract

Gene Set Enrichment Analysis (GSEA) is a computational method that assesses whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. We report the availability of a new version of the Java based software (GSEA-P 2.0) that represents a major improvement on the previous release through the addition of a leading edge analysis component, seamless integration with the Molecular Signature Database (MSigDB) and an embedded browser that allows users to search for gene sets and map them to a variety of microarray platform formats. This functionality makes it possible for users to directly import gene sets from MSigDB for analysis with GSEA. We have also improved the visualizations in GSEA-P 2.0 and added links to a new form of concise gene set annotations called Gene Set Cards. These additions, as well as other improvements suggested by over 3500 users who have downloaded the software over the past year have been incorporated into this new release of the GSEA-P Java desktop program. Availability: GSEA-P 2.0 is freely available for academic and commercial users and can be downloaded from http://www.broad.

Global secretome analysis identifies novel mediators of bone metastasis

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Wfs1 gene deletion causes growth retardation in mice and interferes with the growth hormone pathway

“…For functional analysis and interpretation of expression data we used Gene Set Enrichment Analysis (GSEA) tool (27). This is a recently developed tool to interpret genome-wide expression profiles.…”

“…The sets of genes that are related to the phenotype should show a nonrandom distribution. Based on the distribution of the genes from the lists, an enrichment score is calculated, for estimation of significance level, phenotype-based permutation test procedure is used (27). Again, nominal P values were adjusted for multiple hypotheses testing by calculating false discovery rate (FDR).…”

Genetics of vesicoureteral reflux

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