I have a list of genes that showed up as differentially expressed between patients and controls. I have seen in papers, people performing analyses to see what fraction of genes in a list are related to cancer, using "Ingenuity Pathway Analysis" etc.

I have been unable to use this software in that manner, though, and wanted to ask if anyone is familiar with another way to accomplish this?
<p>Well unfortunately IPA is not a free software, but there is a lot of great free software available. You can try out functional enrichment analysis with GSEA (http://www.broadinstitute.org/gsea/index.jsp) and DAVID (http://david.abcc.ncifcrf.gov/) platforms.</p>

<p>PS. I&#39;ve managed to get GSEA working for RNA-Seq data by using expression table input with log2-transformed FPKM values produced by Tophat-Cuffquant (http://cufflinks.cbcb.umd.edu/manual.html#cuffquant).</p>
