Pathway- and Protein-Interaction-Based Identification
of Disease Specific SNP Sets in Genome-Wide Accociation Studies

Start GWAS Pathway Identifier:
You may download a stand-alone version as runnable JAR file in our downloads section.

Short description:
Today, the use of genome-wide association (GWA) studies is a common approach to identify genetic variants, i.e., single nucleotide polymorphisms (SNPs), in the human genome. GWA studies help to determine the distribution of these variants in different populations and to reveal possible associations to various diseases. Up to now, several studies uncovered SNPs contributing to disease outbreak and progress. Nevertheless, most diseases are caused by the interplay of several SNPs and not by a single one. It is very likely that one SNP out of a significant set of SNPs has no significance itself. So far, several statistical methods have been developed and applied to GWA studies to uncover associations between genotype and phenotype.
In our approach, we suggest the combination of GWAS data with pathway and protein interaction information to increase the association accuracy and to reveal unexpected pathways connected to the disease mechanisms. We start our investigation of associated SNPs on the pathway level and refine our SNP sets with protein interaction information. Finally, we evaluate our SNP sets with a variation of the Fisther's combined statistic and summarized the results in a neatly arranged HTML report which is accomplishes with a graphical representation of the pathways. In addition to the HTML report, CSV files are provided which can easily be used by other applications for further investigations.

First Release: Download the stand-alone version as runnable JAR file.  -   (buechel - 2011-08-05 13:39)

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