Perform Gene Set Enrichment Analysis

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We will now perform gene set enrichment analysis in GenePattern to determine whether our list of SNP associated genes is up or down regulated in a biological phenotype such as skin cancer.

First, launch GenePattern from the GenomeSpace toolbar. Change to the "Modules" tab and search for GSEA.

Once the module is up, drag the gene symbols file from the Galaxy "cut" operation to the "gene sets database file" parameter.

Load "GSE10423.CLS" into the "phenotype labels".

The output of this run will be a zip file which you can save by clicking on the file, then selecting "Save to GenomeSpace".