Question: How To Compute The Significance Of The Overlap Of The Size Of The Intersection Of Two Gene Sets.
0
gravatar for ChIP
5.2 years ago by
ChIP480
Netherlands
ChIP480 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

pathway statistics • 9.6k views
ADD COMMENTlink modified 3 days ago by Vasei20 • written 5.2 years ago by ChIP480
4

Please check these questions:

ADD REPLYlink modified 3 days ago by RamRS18k • written 5.2 years ago by PoGibas4.7k

Dear 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!

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by hammerberlin0

I think you can use bootstrap in this case!

ADD REPLYlink written 3 days ago by Vasei20
2
gravatar for Vikas Bansal
5.2 years ago by
Vikas Bansal2.3k
Berlin, Germany
Vikas Bansal2.3k wrote:

For a quick solution, look at this page.

A web based CGI scripts that computes the

Statistical significance of the overlap between two groups of genes

via the hypergeometric distribution/

ADD COMMENTlink modified 5.2 years ago by Istvan Albert ♦♦ 77k • written 5.2 years ago by Vikas Bansal2.3k
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