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


BACKGROUND
https://sourceforge.net/projects/snpratiotest/
O'Dushlaine
Colm
C
Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Ireland. codushlaine@gmail.com
Kenny
Elaine
E
Heron
Elizabeth A
EA
Segurado
Ricardo
R
Gill
Michael
M
Morris
Derek W
DW
Corvin
Aiden
A
D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D016678:Genome; D055106:Genome-Wide Association Study / Q000379:methods*; D006801:Humans; D010300:Parkinson Disease / Q000235:genetics; D020641:Polymorphism, Single Nucleotide