Downstream target genes expression analysis (RNA-Seq)

Question

[Nicolas Rosewick]

Hi,

I've 32 samples expression data (RNA-Seq) in which 4 of them have a specific gene that is mutated (MUT samples). I want to asses wheter downstream targets ( direct or indirect) of this specific gene have a dysregulated expression. So my idea was to first perform DE analysis to extract the up/down genes in the 4 MUT samples compared to the other 28 samples. After that, to cross these up/down genes with known targets of my gene of interest ( using Biogrid or other interaction database ). Sub question : How to check the indirect targets ?

Do you think it's a good way to do that ? Anyone has other ideas ?

Thanks