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
Gsea Mouse Gene Set
RNA-Seq; Gene expression
Gsea Gene Set Database
Second, when I opened the downloaded.jnlp file, GSEA does open fine, but when the Load Data button is clicked on, there is no pop up window for input files. I have the latest Java (9.0) installed on my Mac (OS X 10.10). Any discussion on this will be appreciated! You advance to the GSEA Finals with 50 of the world’s best student entrepreneurs. Win the award, become the EO GSEA Student Champion and receive. Download the files from the GSEA web site, or create your own chip file. The expression dataset, gene sets, and chip annotation files all contain lists of features (genes or probes) to be analyzed. It is critical that you use the same feature (gene or probe) identifiers across all. UNLABELLED: 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.
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
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
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
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
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
PMID: 17644558
Download and documentation
- Source:http://software.broadinstitute.org/gsea/
downloads.jsp - Documentation:http://software.broadinstitute.org/cance
r/software/gsea/wiki/index.php/Main_Page - Home page:http://software.broadinstitute.org/gsea/
index.jsp - Data:http://software.broadinstitute.org/gsea/
msigdb/index.jsp - Links:http://www.broadinstitute.org/cancer/sof
tware/gsea/wiki/index.php/Using_RNA-
seq_Datasets_with_GSEA