Optimizing gene scores for pathway enrichment

Background: Pathway enrichment is an important analysis tool in large scale biology, in particular in GWAS experiments. We recently published a tool to perform such analysis as a downstream part of GWAS analysis. However, the method contains a lot of parameters that might affect the power of the method.

Goal: we will try to optimize parameters for gene score calculation to improve pathway prediction. We will evaluate on a large collection of GWAS and hopefully uncover new/different pathways in the process.