I'm studying two cancers in the same tissue and wanted to identify common pathways in both diseases based on microarray and RNA-Seq expression data.
I could run separate enrichment and pathway analysis on each disease and simply observe which pathways are common.
My question is: is there a way to use the intersection of differentially expressed genes in each disease in any kind of enrichment analysis?
I tried running over-representation tests and GSEA on the intersection list but since it is quite small -- around 100 DEGs -- all results came out statistically insignificant. Perhaps I'm using the wrong background list? I've tried the background list obtained after employing typical non-specific filtering techniques. It works well for each individual disease but not with the intersection of GDEs.
Someone suggested that I use the union of GDEs as background but I couldn't find a strong rationale for that (or any good reference on this, for that matter.)