Hello, I have a data for pair-wise interactions between genes. I have taken the top 1000 interactions (ordered based on some value) and found that X no. of interactions in which Gene_1 is hypo methylated and Gene_2 is Up-regulated.

My objective is to prove that the X no. of interactions (in the ordered set) is significantly higher than a random set of interactions. For this, I randomized the interactions 1000 times and calculated the interactions for which Gene1 is hypo methylated and Gene2 is Up-regulated. My question is how to get a p-value for this permutation? Kindly help. Thanks.

Thats great, Merci beaucoup!

Although it usually will not make much difference, I would add that there is an argument for estimating the permutation p-value adding 1 to the numerator and denominator (so that

`p-val = n + 1 / m + 1`

where n is your number of hits higher or equal to your threshold and m is the number of permutations) (see this reference)