Supportness of the protein complex standards in PPI networks

ABSTRACT A protein complex is a collection of two or more associated proteins that interact with each other in a stable long-term interaction. Protein complexes have essential roles in regulatory processes, cellular functions and signaling cascades. This paper examines how well-known collections of protein complexes are supported in protein–protein interaction (PPI) networks, i.e. whether they form connected subnetworks in a particular PPI network. For that purpose, we apply a variable neighbourhood search (VNS) metaheuristic algorithm for adding the minimum number of interactions in order to support protein complexes. Experimental results obtained on several PPI networks (BioGRID, WI-PHI and String) and four protein complex standards (MIPS, TAP06, SGD and CYC2008) show that considered networks do not include enough PPIs to support all complexes from complex standards. Deeper analysis indicates that there exists common PPIs which are probably missing in the considered networks. These findings can be useful for further biological interpretation and developing of PPI prediction models.