Hello!
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.
Thank you!
Seems to me the other thing you could do is do pathway analysis for each set of genes, see if the same pathways come up.