Hi Zoozeal,

I cannot understand your question well. The fist and second shell interacting partners just mean the first and second neighbor interactors of the given nodes (genes/proteins)? If it is the case, there is not a unified criterion for a limit for this. You could either only consider the experimentally-evidenced interacting partners due to the really high false positive results from the computationally-predictive methods, or take into consideration the upstream regulators and downstream effectors. The current studies on protein-protein interactions are in a very messy state & just at the beginning stage. More interactions should be identified and refined.

Best,

Yanshi

Thanks for your insights Yanshi.