Gowinda
|
Application data |
|
| Created by | Robert Kofler |
|---|---|
| Biological application domain(s) | Genomics, Population genetics, Population Genomics, Sequencing |
| Principal bioinformatics method(s) | Functional enrichment, Ontology comparison, Genome-wide association study |
| Created at | VetMedUni Vienna |
| Maintained? | Yes |
| Input format(s) | GTF, VCF, Pileup |
| Software features | Multicore |
| Programming language(s) | Java |
| Licence | Mozilla Public License |
| Operating system(s) | Mac OS X, Linux, Windows |
Summary: Gowinda: unbiased analysis of gene set enrichment for Genome Wide Association Studies
"Error: no local variable "counter" was set." is not a number.
Description
Gowinda is a multi-threaded Java application that allows an unbiased analysis of gene set enrichment for Genome Wide Association Studies. Classical 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. Gowinda has been 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.
Links
References
none specified
To add a reference for Gowinda, enter the PubMed ID in the field below and click 'Add'.
Search for "Gowinda" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
