Hello, I have quite a strange question to ask regarding RNA Sequencing differentially expressed list...

I have two DE comparisons:

(1) Disease line with deleted SNP vs disease line without deleted SNP

(2) Disease line with deleted SNP vs normal line with deleted SNP

There might be underlying disease background (interactions with other disease SNPs) in comparison 1 that is affecting my results.

I hope to do a venn diagram (maybe even a pathway comparison or to extract a gene list) between these two comparisons, but have no idea how to start.

I attached a schematic to make it clearer. I will sincerely appreciate any help, thank you!