we have done microarray and chip-seq assays for a human cell line before and after inhibition of a cell surface protein. Analyzing the microarray results, we found almost 750 genes up-regulated (over-expressed) following the inhibition. Chip-seq of H3k27ac mark revealed almost 2000 genes associated with the H3K27ac peaks. I overlapped the results from both assays and found only 25 genes in common. I want to obtain a p-value to conclude weather acetylation of H3k27 induced the expression of up-regulated genes obtained from the microarray. HOW can I calculate the p-value using Hypergeometric test???
According to Biogrid (3.4.163- August 2018), there are 22,792 unique genes in human cells.
If you seek a simple and fast tool: http://systems.crump.ucla.edu/hypergeometric/
If you want to write your own script, I can only suggest to look on sites such as biostars and stackoverflow:
https://stackoverflow.com/questions/8382806/hypergeometric-test-phyper
https://www.biostars.org/p/90662/
https://www.biostars.org/p/128701/
It's called Fisher Exact test by most people I know. It's named for Ronald Fisher, the rock-star geneticist of the 20th century.
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