Journal Article

The SNP ratio test: pathway analysis of genome-wide association datasets

Colm O'Dushlaine, Elaine Kenny, Elizabeth A. Heron, Ricardo Segurado, Michael Gill, Derek W. Morris and Aiden Corvin

in Bioinformatics

Volume 25, issue 20, pages 2762-2763
Published in print October 2009 | ISSN: 1367-4803
Published online July 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp448
The SNP ratio test: pathway analysis of genome-wide association datasets

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Summary: We present a tool that assesses the enrichment of significant associations from genome-wide association studies (GWAS) in a pathway context. The SNP ratio test (SRT) compares the proportion of significant to all SNPs within genes that are part of a pathway and computes an empirical P-value based on comparisons to ratios in datasets where the assignment of case/control status has been randomized. We applied the SRT to a Parkinson's disease GWAS dataset, using the KEGG database, revealing significance for Parkinson's disease and related pathways.

Availability: https://sourceforge.net/projects/snpratiotest/

Contact: codushlaine@gmail.com; colm.odushlaine@tcd.ie

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1641 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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