I am working with an in silico model to measure the distances between drugs targets and disease proteins of a disease. I would want to compare these distances with the distances of random networks but I don't know which is the best way to do the comparison. For instance, if I have 300 drug targets and 500 disease proteins mapped in the interactome and I want to measure the distance between them and then compare to random networks with the same features.
How do I generate these random networks? Choosing the same number of drug targets (300) and disease genes (500) randomly in my referral network? Choosing the same number of nodes (300 and 500) and the same number of links?
I'd appreciate your help!