Identification of function modules in protein-protein interaction networks by modularity optimization method

It is of great significance to understand the organization and function of the biological system by identifying function modules in protein-protein interaction (PPI) networks. One of important features of PPI networks is large-scale. In this paper, we propose the modules detection method for PPI networks based on modularity optimization. The biolbiologicalogical explanations of the función modules are analyzed based on Gene Ontology(GO). The experimental results show that most of the detected modules have high match ratio and biological significance no matter what the ontology analysis form. In terms of node loss ratio, the modularity optimization methods are much better than the clique percolation clustering method(CPM).