Protein complex detection algorithm based on multiple topological characteristics in PPI networks

Abstract

Detecting protein complexes from available protein–protein interaction (PPI) networks is an important task, and several related algorithms have been proposed. These algorithms usually consider a single topological metric and ignore the rich topological characteristics and inherent organization information of protein complexes. However, the effective use of such information is crucial to protein complex detection. To overcome this deficiency, this study presents a heuristic clustering algorithm to identify protein complexes by fully exploiting the topological information of PPI networks. By considering the clustering coefficient and the node degree, a new nodal metric is proposed to quantify the importance of each node within a local subgraph. An iterative paradigm is used to incrementally identify seed proteins and expand each seed to a cluster. First, among the unclustered nodes, the node with the highest nodal metric is selected as a new seed. Then, the seed is expanded to a cluster by adding candidate nodes recursively from its neighbors according to both the density of the cluster and the connection between a candidate node and the cluster. The experimental results demonstrate that the proposed algorithm outperforms other competing algorithms in terms of F-measure and accuracy.