Clustering based on multiple biological information: approach for predicting protein complexes

Protein complexes are a cornerstone of many biological processes. Protein-protein interaction (PPI) data enable a number of computational methods for predicting protein complexes. However, the insufficiency of the PPI data significantly lowers the accuracy of computational methods. In the current work, the authors develop a novel method named clustering based on multiple biological information (CMBI) to discover protein complexes via the integration of multiple biological resources including gene expression profiles, essential protein information and PPI data. First, CMBI defines the functional similarity of each pair of interacting proteins based on the edge-clustering coefficient and the Pearson correlation coefficient. Second, CMBI selects essential proteins as seeds to build the protein complexes. A redundancy-filtering procedure is performed to eliminate redundant complexes. In addition to the essential proteins, CMBI also uses other proteins as seeds to expand protein complexes. To check the performance of CMBI, the authors compare the complexes discovered by CMBI with the ones found by other techniques by matching the predicted complexes against the reference complexes. The authors use subsequently GO::TermFinder to analyse the complexes predicted by various methods. Finally, the effect of parameters T and R is investigated. The results from GO functional enrichment and matching analyses show that CMBI performs significantly better than the state-of-the-art methods.