Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies.
CONCLUSIONS
An analysis of gene set [e.g. Gene Ontology (GO)] 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 single-nucleotide polymorphisms resulting in a higher probability of being sampled and (ii) overlapping genes are sampled in clusters. Herein, we introduce Gowinda, a software specifically designed to test for enrichment of gene sets in GWA studies. We show that 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 datasets requires millions of permutations, we use multi-threading to keep computation times reasonable.


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


BACKGROUND
christian.schloetterer@vetmeduni.ac.at


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


RESULTS
http://code.google.com/p/gowinda/wiki/VALIDATION.
Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, A-1210 Wien, Austria.
Robert
R
Kofler
Christian
C
Schlötterer
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004331:Drosophila melanogaster / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods*; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D011336:Probability; D012984:Software