I have a gtex model file, I noticed that there are several SNPs that are regulation Gene A expression in more than one tissues. Is there any method to evaluate such a condition and get function information from it?
This is how my file look like:
So for this:
SNP1(rs1041770) and SNP2(rs12628452) regulating gene ENSG00000283633 is present in tissue adipose subcutaneous but not in adipose visceral.
I was reading research and there is a research being done on eQTL using bipartite network:
This is what the paper states: For each of the 13 tissues, we represented the significant eQTL as a bipartite network, with nodes representing either SNPs or genes and edges representing significant SNP–gene associations
But I want to do it for all tissues, So I have develop network for each tissue: how can I see the commonality and differences between them. Can anyone provide more guidance on this. I am new to network analysis and functional annotation work. Or any other method that can evaluate this kind of relationships for snps across tissues.