Pattern Discovery in Protein Networks Reveals High-Confidence Predictions of Novel Interactions

Pattern discovery in protein interaction networks can reveal crucial biological knowledge on the inner workings of cellular machinery. Although far from complete, extracting meaningful patterns from proteomic networks is a non-trivial task due to their size-complexity. This paper proposes a computational framework to efficiently discover topologically-similar patterns from large proteomic networks using Particle Swarm Optimization (PSO). PSO is a robust and low-cost optimization technique that demonstrated to work effectively on the complex, mostly sparse proteomic networks. The resulting topologically-similar patterns of close proximity are utilized to systematically predict new high-confidence protein-protein interactions (PPIs). The proposed PSO-based PPI prediction method (3PI) managed to predict high-confidence PPIs, validated by more than one computational/experimental source, through a proposed PPI knowledge transfer process between topologically-similar interaction patterns of close proximity. In three case studies, over 50% of the predicted interactions for EFGR, ERBB2, ERBB3, GRB2 and UBC are overlapped with publically available interaction databases, ~80% of the predictions are found among the Top 1% results of another PPI prediction method and their genes are significantly co-expressed across different tissues. Moreover, the only single prediction example that did not overlap with any of our validation sources was recently experimentally supported by two PubMed publications.