Question: GeneOverlap - overlap of DE genes from 2 or 3 RNA-Seq experiments
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gravatar for Chris Gene
2.8 years ago by
Chris Gene60
United Kingdom
Chris Gene60 wrote:

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.
Eg.
Dataset A:
3500 DE genes
12000 genes expressed in tissue (background)

Dataset B:
2500 DE genes
11500 genes expressed in tissue (background)

Dataset C:
800 DE genes
11600 genes xpressed in tissue (background)

Overlap for A x B x C:
150 DE genes
11000 genes in background

Thanks!

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Chris Gene60

Sorry, but did you have a question?

ADD REPLYlink written 2.8 years ago by Sean Davis25k

How can I determine whether the overlap is statistically significant? Is there an enrichment?

ADD REPLYlink written 2.8 years ago by Chris Gene60
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