Send to:

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2008 Dec 1;24(23):2784-5. doi: 10.1093/bioinformatics/btn516. Epub 2008 Oct 14.

GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies.

Author information

  • 1Norwegian Computing Center, Oslo, Norway, Department of Pharmacology, University of Mainz, Mainz, Germany.


The power of genome-wide SNP association studies is limited, among others, by the large number of false positive test results. To provide a remedy, we combined SNP association analysis with the pathway-driven gene set enrichment analysis (GSEA), recently developed to facilitate handling of genome-wide gene expression data. The resulting GSEA-SNP method rests on the assumption that SNPs underlying a disease phenotype are enriched in genes constituting a signaling pathway or those with a common regulation. Besides improving power for association mapping, GSEA-SNP may facilitate the identification of disease-associated SNPs and pathways, as well as the understanding of the underlying biological mechanisms. GSEA-SNP may also help to identify markers with weak effects, undetectable in association studies without pathway consideration. The program is freely available and can be downloaded from our website.

[PubMed - indexed for MEDLINE]
Free full text
PubMed Commons home

PubMed Commons

How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire
    Loading ...
    Write to the Help Desk