I computed Gene ontology semantic similarity as follows
I took the genes from two different co-expression networks from gene expression dataset. For example
Module 1 : 30 genes
Module 2: 20 genes
Once I had them in hand I used gene ontology software and annotate the genes using biological process category. Later I obtained GO IDs and used GOSEMSIM R package to compute similarities ranges from 0 to 1. This is the data from experiment. Now I want to test GO similarity significance as follows.
Generate the two random gene sets of the same sizes and compute GO similarity and finally caluculate the P-value by comparing it with GO similarities which are obtained from real data. I am not getting the way how to do it? specifically how to select the random gene sets of same sizes and calculate the P-values? Can any body please let me know the exact procedures to do this ?