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Hi,

How can we calculate hyper geometric probability for a set of gene , how can we know the total number of gene , and the number of gene in that specific pathway , and can we use more than one database for calculation the hyper geometric probability. can we calculate the hyper geometric probability manually ?

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You can use this nice webserver to do the task, and run across multiple pathway collections

http://bioinfo.vanderbilt.edu/webgestalt/

Sounds like https://github.com/endrebak/goverlap should do what you want.