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.