title: 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.
  
  
  BACKGROUND
  GSEA-P 2.0 is freely available for academic and commercial users and can be downloaded from http://www.broad.mit.edu/GSEA
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Aravind
authors.initials: A
authors.lastname: Subramanian
authors.forename: Heidi
authors.initials: H
authors.lastname: Kuehn
authors.forename: Joshua
authors.initials: J
authors.lastname: Gould
authors.forename: Pablo
authors.initials: P
authors.lastname: Tamayo
authors.forename: Jill P
authors.initials: JP
authors.lastname: Mesirov
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D020869:Gene Expression Profiling; D008954:Models, Biological; D011381:Programming Languages; D011506:Proteins / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins