Question: How To Compute The Significance Of The Overlap Of The Size Of The Intersection Of Two Gene Sets.

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ChIP •

**480**wrote:Hi!

I have a genelist from a KEGG pathway say TGFb signalling pathway, that has 80 genes in it (set A). and I have second list of genes with me which accounts for 45 genes (set B), and the overlap between the two sets is of 15 genes.

How can I get a p-value associated with this overlap?

Has anyone done this before?

I think, phyper of R can be applied to this .......

Thank you

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18k• written 5.2 years ago by PoGibas ♦4.7kDear folks,

I wonder what method would fit best to compute the significance of the overlap between three groups of genes? For calculation the p-Values I used the Fisher's exact test. If I understand right, the Fisher's exact test is just practical for a comparison of two groups of genes, right?!

Thanks!

0I think you can use bootstrap in this case!

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