Achieving high k-coverage and k-consistency in global alignment of multiple PPI networks

Abstract

Alignment among protein-protein interaction (PPI) networks largely benefits our understanding in biological researches as it contributes greatly to the uncovering of important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. Global alignment of multiple PPI networks aims at clustering functionally conserved proteins throughout different species, where most traditional methods attempt to achieve results with high overall coverage and consistency. However little attention was paid on the deeper level criteria of k-coverage and especially the k-consistency that we additionally conducted for evaluations, where k indicates the number of species that the proteins in a cluster belong to. In this paper, we propose a novel approach for global alignment of multiple PPI networks which achieved high k-coverage and k-consistency simultaneously in addition to conventional criteria. The evaluations demonstrate the preferable comprehensive strength of our approach against other three state-of-the-art methods on six datasets composed of various numbers of PPI networks from five species.