I've got rna-seq expression data in two subtypes of cancer divided into two smaller groups each (finally I am having 4 groups to compare). I would like to compare all 4 groups at once to see gene profiles that are common and different between all these groups. I'd like to ask you what would be suggested method. My data is large, as it has 20k genes. I've already tried different variants of hierarchical clustering, but I get the whole picture of all 20k. There are visible patterns, but not clearly separated and I would need to filter the most differentiating genes manually. Is there any other option to contrast all these 4 groups at once and filter out genes that differentiate them well?
I'll appreciate your help and advices very much. Thank you in advance.