GeneOverlap - overlap of DE genes from 2 or 3 RNA-Seq experiments

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7.8 years ago

Chris Gene ▴ 80

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!

RNA-Seq R GeneOverlap Hypergeometric test • 2.1k views

ADD COMMENT • link 7.8 years ago by Chris Gene ▴ 80

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Sorry, but did you have a question?

ADD REPLY • link 7.8 years ago by Sean Davis 26k

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

ADD REPLY • link 7.8 years ago by Chris Gene ▴ 80

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