A Novel Core-Attachment-Based Method to Identify Dynamic Protein Complexes Based on Gene Expression Profiles and PPI Networks

Cellular functions are always performed by protein complexes. At present, many approaches have been proposed to identify protein complexes from protein-protein interaction (PPI) networks. Some approaches focus on detecting local dense subgraphs in PPI networks which are regarded as protein-complex cores, then identify protein complexes by including local neighbors. However, from gene expression profiles at different time points or tissues it is known that proteins are dynamic. Therefore, identifying dynamic protein complexes should become very important and meaningful. In this study, a novel core-attachment-based method named CO-DPC to detect dynamic protein complexes is presented. First, CO-DPC selects active proteins according to gene expression profiles and the 3-sigma principle, and constructs dynamic PPI networks based on the co-expression principle and PPI networks. Second, CO-DPC detects local dense subgraphs as the cores of protein complexes and then attach close neighbors of these cores to form protein complexes. In order to evaluate the method, the method and the existing algorithms are applied to yeast PPI networks. The experimental results show that CO-DPC performs much better than the existing methods. In addition, the identified dynamic protein complexes can match very well and thus become more meaningful for future biological study.