title: Identifying protein complexes based on brainstorming strategy.
abstract: Protein complexes comprising of interacting proteins in protein-protein interaction network (PPI network) play a central role in driving biological processes within cells. Recently, more and more swarm intelligence based algorithms to detect protein complexes have been emerging, which have become the research hotspot in proteomics field. In this paper, we propose a novel algorithm for identifying protein complexes based on brainstorming strategy (IPC-BSS), which is integrated into the main idea of swarm intelligence optimization and the improved K-means algorithm. Distance between the nodes in PPI network is defined by combining the network topology and gene ontology (GO) information. Inspired by human brainstorming process, IPC-BSS algorithm firstly selects the clustering center nodes, and then they are separately consolidated with the other nodes with short distance to form initial clusters. Finally, we put forward two ways of updating the initial clusters to search optimal results. Experimental results show that our IPC-BSS algorithm outperforms the other classic algorithms on yeast and human PPI networks, and it obtains many predicted protein complexes with biological significance.
authors.affiliation: School of Computer, Central China Normal University, Wuhan 430079, China; Collaborative & Innovative Center for Educational Technology, Central China Normal University, Wuhan 430079, China. Electronic address: xjshen@mail.ccnu.edu.cn.
authors.forename: Xianjun
authors.initials: X
authors.lastname: Shen
authors.affiliation: School of Computer, Central China Normal University, Wuhan 430079, China. Electronic address: dreamxiaojin@163.com.
authors.forename: Jin
authors.initials: J
authors.lastname: Zhou
authors.affiliation: School of Computer, Central China Normal University, Wuhan 430079, China. Electronic address: yili@mails.ccnu.edu.cn.
authors.forename: Li
authors.initials: L
authors.lastname: Yi
authors.affiliation: School of Computer, Central China Normal University, Wuhan 430079, China. Electronic address: xh29@drexel.edu.
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Hu
authors.affiliation: School of Computer, Central China Normal University, Wuhan 430079, China. Electronic address: tthe@mail.ccnu.edu.cn.
authors.forename: Tingting
authors.initials: T
authors.lastname: He
authors.affiliation: School of Computer, Central China Normal University, Wuhan 430079, China. Electronic address: jcyang@mail.ccnu.edu.cn.
authors.forename: Jincai
authors.initials: J
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps / Q000235:genetics*; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics
keywords: Brainstorming strategy; Gene ontology; Protein complex; Protein-protein interaction network