I am comparing 3 differentially expressed (DE) gene datasets. Ideally I would want to do a 3-way comparison, but breaking it down into pairwise would be fine too.
As I understand, GeneOverlap functions in a way similar to a hypergeometric test, and does not take into account the background of genes expressed.
3500 DE genes
12000 genes expressed in tissue (background)
2500 DE genes
11500 genes expressed in tissue (background)
800 DE genes
11600 genes xpressed in tissue (background)
Overlap for A x B x C:
150 DE genes
11000 genes in background