Protein complexes detection based on node local properties and gene expression in PPI weighted networks

Background Identifying protein complexes from protein-protein interaction (PPI) networks is a crucial task, and many related algorithms have been developed. Most algorithms usually employ direct neighbors of nodes and ignore resource allocation and second-order neighbors. The effective use of such information is crucial to protein complex detection. Result Based on this observation, we propose a new way by combining node resource allocation and gene expression information to weight protein network (NRAGE-WPN), in which protein complexes are detected based on core-attachment and second-order neighbors. Conclusions Through comparison with eleven methods in Yeast and Human PPI network, the experimental results demonstrate that this algorithm not only performs better than other methods on 75% in terms of f-measure+, but also can achieve an ideal overall performance in terms of a composite score consisting of five performance measures. This identification method is simple and can accurately identify more complexes.

Automated summary

In this study, a new method is proposed for detecting protein complexes by combining node resource allocation and gene expression information to weight the protein network. Experimental results show that this method outperforms other methods in terms of performance and can accurately identify more complexes.