Hello everybody! We have modified cells with the lentiviral construction and then analyzed the result by RNAseq. I've made gene set enrichment analysis in R-package fgsea. And obtained the result, which I find difficult to interpret. The most statistically significant pathways appear to be a cell immune response to virus attack. How can that be, if I compare two groups, which both are transfected with the viruses?
We keep cells for 2 days after transfection then extracted RNA. Surely, immune response should be expressed. But I supposed it should be leveled off by comparing both transfected groups.
GSEA uses completely arbitrary generated gene sets. You should look what genes are inside the geneset, could it be that your lentiviral modification affects these genes directly? Aka is not result of virus but effect of modification itself?
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