Peer-Reviewed Journal Details
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O'Dushlaine, C.,Kenny, E.,Heron, E. A.,Segurado, R.,Gill, M.,Morris, D. W.,Corvin, A.
2009
October
Bioinformatics
The SNP ratio test: pathway analysis of genome-wide association datasets
Published
()
Optional Fields
25
2020
2762
3
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/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/
1367-4811 (Electronic)13
http://www.ncbi.nlm.nih.gov/pubmed/19620097
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