So I am working on reconstructing a gene regulatory network for Glioma/Glioblastoma starting from RNA-seq data. the data I have is for different patients at different stages of the disease (different grades 2, 3 and 4).
I ran a differential expression analysis and extracted the DE genes in-between the different grades. (instead of disease vs control, I ran DESEq2 with the grade as the factor) ie. grade 4 vs grade 2, 3 vs 2 and 4 vs 3.
I got the following results:
I want to make sure that it makes sense to take a subset of common genes like this for the purpose of reconstructing a regulatory network, and if the numbers I have are logical in this context.
N.B: The 8 genes from the subset do seem to have a relationship with the disease from the literature, although there is no direct regulation or signaling pathway between them.