I've a list of genes (~100) that are mutated in my trated samples compared to untreated. I've also RNA-Seq data from these samples. Now I want to know the potential effect of these mutations on gene expression of direct and indirect target genes of my list of mutated genes. My idea was to use pathway information to check the expression of direct targets of my 100-mutated-genes and check if they are up/down regulated.. My final aim is to detect specific target genes and biological pathways that are perturbated due to the mutateted genes.
Any advice or ideas ?