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GSEA (UCSD)

GSEA (UCSD)

GSEA (Gene Set Enrichment Analysis) is a tool for gene enrichment analysis. The GSEA algorithm assesses differences between gene sets and uses the Molecular Signatures Database (MSigDB) for annotation.

Topic

RNA-Seq; Gene expression

Details

  • Operation: Gene-set enrichment analysis
  • Software interface: Graphical user interface
  • Language: Java
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Other
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: National Cancer Institute (NCI); Informatics Technology for Cancer Research (ITCR).
  • Contact: gsea-team _at_ broadinstitute.org
  • Collection: -

Publications

Rothgänger J, Weniger M, Weniger T, Mellmann A, Harmsen D "Ridom TraceEdit: a DNA trace editor and viewer." Bioinformatics https://doi.org/
PMID: 16357036


Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstråle M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN, Altshuler D, Groop LC "PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes." Nat Genet. 2003 Jul;34(3):267-73. https://doi.org/10.1038/ng1180
PMID: 12808457


Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP "Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles." Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. 10.1073/pnas.0506580102. Epub 2005 Sep 30. https://doi.org/10.1073/pnas.0506580102
PMID: 16199517
PMCID: PMC1239896


Bild A, Febbo PG "Application of a priori established gene sets to discover biologically important differential expression in microarray data." Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15278-9. Epub 2005 Oct 17. https://doi.org/10.1073/pnas.0507477102
PMID: 16230612
PMCID: PMC1266131


Subramanian A, Kuehn H, Gould J, Tamayo P, Mesirov JP "GSEA-P: a desktop application for Gene Set Enrichment Analysis." Bioinformatics. 2007 Dec 1;23(23):3251-3. Epub 2007 Jul 20. https://doi.org/10.1093/bioinformatics/btm369
PMID: 17644558


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