A core-attachment based method to detect protein complexes in PPI networks

How to detect protein complexes is an important and challenging task in post genomic era. As the increasing amount of protein-protein interaction (PPI) data are available, we are able to identify protein complexes from PPI networks. However, most of current studies detect protein complexes based solely on the observation that dense regions in PPI networks may correspond to protein complexes, but fail to consider the inherent organization within protein complexes. To provide insights into the organization of protein complexes, this paper presents a novel core-attachment based method (COACH) which detects protein complexes in two stages. It first detects protein-complex cores as the "hearts" of protein complexes and then includes attachments into these cores to form biologically meaningful structures. We evaluate and analyze our predicted protein complexes from two aspects. First, we perform a comprehensive comparison between our proposed method and existing techniques by comparing the predicted complexes against benchmark complexes. Second, we also validate the core-attachment structures using various biological evidence and knowledge. Our proposed COACH method has been applied on two different yeast PPI networks and the experimental results show that COACH performs significantly better than the state-of-the-art techniques. In addition, the identified complexes with core-attachment structures are demonstrated to match very well with existing biological knowledge and thus provide more insights for future biological study.