General Information
| Description | An algorithm to identify cell types, tissues and pathways affected by risk loci |
| Homepage | http://broadinstitute.org/mpg/snpsea |
Publications
SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci
Summary:
We created a fast, robust and general C++ implementation of a single-nucleotide polymorphism (SNP) set enrichment algorithm to identify cell types, tissues and pathways affected by risk loci. It tests trait-associated genomic loci for enrichment of specificity to conditions (cell types, tissues and pathways). We use a non-parametric statistical approach to compute empirical P-values by comparison with null SNP sets. As a proof of concept, we present novel applications of our method to four sets of genome-wide significant SNPs associated with red blood cell count, multiple sclerosis, celiac disease and HDL cholesterol.
Availability and implementation:
http://broadinstitute.org/mpg/snpsea
Contact:
soumya@broadinstitute.org
Supplementary information:
Supplementary Data are available at Bioinformatics online.
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