title: Identifying hierarchical and overlapping protein complexes based on essential protein-protein interactions and "seed-expanding" method.
abstract: Many evidences have demonstrated that protein complexes are overlapping and hierarchically organized in PPI networks. Meanwhile, the large size of PPI network wants complex detection methods have low time complexity. Up to now, few methods can identify overlapping and hierarchical protein complexes in a PPI network quickly. In this paper, a novel method, called MCSE, is proposed based on λ-module and "seed-expanding." First, it chooses seeds as essential PPIs or edges with high edge clustering values. Then, it identifies protein complexes by expanding each seed to a λ-module. MCSE is suitable for large PPI networks because of its low time complexity. MCSE can identify overlapping protein complexes naturally because a protein can be visited by different seeds. MCSE uses the parameter λ_th to control the range of seed expanding and can detect a hierarchical organization of protein complexes by tuning the value of λ_th. Experimental results of S. cerevisiae show that this hierarchical organization is similar to that of known complexes in MIPS database. The experimental results also show that MCSE outperforms other previous competing algorithms, such as CPM, CMC, Core-Attachment, Dpclus, HC-PIN, MCL, and NFC, in terms of the functional enrichment and matching with known protein complexes.
authors.affiliation: College of Information Science and Technology, Hunan Agricultural University, Changsha 410128, China ; School of Information Science and Engineering, Central South University, Changsha 410083, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Ren
authors.affiliation: Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Changsha 410128, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhou
authors.affiliation: School of Information Science and Engineering, Central South University, Changsha 410083, China.
authors.forename: Jianxin
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D030562:Databases, Protein; D046912:Multiprotein Complexes / Q000378:metabolism*; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*
chemical_list: D046912:Multiprotein Complexes; D029701:Saccharomyces cerevisiae Proteins