In recent years, many protein complex mining algorithms, such as classical clique percolation (CPM) method and markov clustering (MCL) algorithm, have developed for protein-protein interaction network. However, most of the available algorithms primarily concentrate on mining dense protein subgraphs as protein complexes, failing to take into account the inherent organizational structure within protein complexes. Thus, there is a critical need to study the possibility of mining protein complexes using the topological information hidden in edges. Moreover, the recent massive experimental analyses reveal that protein complexes have their own intrinsic organization.