Abstract
BackgroundHow 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.ResultsTo 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.ConclusionOur 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.
Highlights
How to detect protein complexes is an important and challenging task in post genomic era
Comparative evaluation In this subsection, we compared the performance of our core-attachment based method (COACH) method with other three competing algorithms, DPClus [13], DECAFF [14] and MCL [9,18,27], using DIP data
Note that for fair comparisons, we turned off the filtering step in DECAFF because it used the functional information to filter away possible false positive complexes while other techniques only used topological properties of protein-protein interaction (PPI) networks
Summary
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. One important task in proteomics is to detect protein complexes based on the PPI data generated by various experimental technologies, e.g., yeast-two-hybrid [1], affinity purification [2,3,4] and others. Protein complexes are molecular aggregations of proteins assembled by multiple protein-protein interactions. Many proteins are functional only after they are assembled into a protein complex and interact with other proteins in this complex. Multiple-protein complexes are key molecular entities to perform cellular functions. The complex 'RNA polymerase II' transcribes genetic informa-
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
