Hello all, I have RNA- seq data from different untreated cancer cell lines (obtained from different parts of the body). Some are responsive to treatment whereas others are not. I want to find a common pattern of genes or pathways that are modulated in both groups. I have already performed differential expression analysis and pathway analysis like GSEA, DAVID etc, and some common patterns have started to emerge. I would like to know if there are any tools or methodology that you would apply to these data sets to dig out interesting data?