The SNP ratio test: pathway analysis of genome-wide association datasets.
other · Level V
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- Record sourced from PubMed, PMID 19620097.
- Also identified by DOI 10.1093/bioinformatics/btp448.
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Abstract
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. https://sourceforge.net/projects/snpratiotest/
Medical subject headings
- Computational Biology
- Genome
- Genome-Wide Association Study
- Polymorphism, Single Nucleotide