In this paper, we propose to apply non-uniform weighs to the genes in the pathway based analysis and present two weighting schemes for the genes in pathway. Specifically, we incorporate our weighting schemes into the global test pathway based analysis approach and investigate the effects of our weighting schemes. We observe that when non-uniform weights are applied, some originally lower ranked pathways are elevated to the high ranks, prediction performances of the selected genes are improved, and some genes associated with the related phenotype are identified, which are missed by uniform weighting approach.
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