I have a little side project where I am working on the TCGA expression data. In another cohort, we found some interesting patterns of gene expression with some clear groups based on two other genes. I would like to compare now the expression profile dependent on the other two genes (A and B), or more specifically their difference. In a first naïve approach I calculated correlations for A and B respectively with all other genes (X, Y, Z ...). Taking the absolute difference of the correlation [cor(A) - cor(B)] for X, Y, Z... I do indeed get the most differentially expressed genes. I was wondering now if there is a better approach to this? How would you proceed afterward? Network analysis? Ontology? (any software recommendations? I prefer R primarily).
Thanks a lot.