Sunday, May 27, 2012

Fwd: Gowinda: unbiased analysis of gene set enrichment for Genome Wide Association Studies

Fwd: please follow footer link
Gowinda: unbiased analysis of gene set enrichment for Genome Wide Association Studies:

Summary: An analysis of gene set (e.g.: Gene Ontology) enrichment assumes that all genes are sampled independently from each other with the same probability. These assumptions are violated in Genome Wide Association (GWA) studies since (i) longer genes typically have more SNPs resulting in a higher probability of being sampled and (ii) overlapping genes are sampled in clusters. Here we introduce Gowinda, a software specifically designed to test for enrichment of gene sets in GWA studies. We show that Gene Ontology (GO) tests on GWA data could result in a substantial number of false positive GO terms. Permutation tests implemented in Gowinda eliminate these biases, but maintain sufficient power to detect enrichment of GO terms. Since, sufficient resolution for large data sets requires millions of permutations, we use multi-threading to keep computation times reasonable.

Availability and implementation: Gowinda is implemented in Java (v1.6) and freely available on http://code.google.com/p/gowinda/

Contact:christian.schloetterer@vetmeduni.ac.at

Supplementary information: Manual: http://code.google.com/p/gowinda/wiki/Manual Test data and tutorial: http://code.google.com/p/gowinda/wiki/Tutorial Validation: http://code.google.com/p/gowinda/wiki/Validation



(Original Post: Bioinformatics - Advance Access.)