title: A novel algorithm for detecting protein complexes with the breadth first search.
abstract: Most biological processes are carried out by protein complexes. A substantial number of false positives of the protein-protein interaction (PPI) data can compromise the utility of the datasets for complexes reconstruction. In order to reduce the impact of such discrepancies, a number of data integration and affinity scoring schemes have been devised. The methods encode the reliabilities (confidence) of physical interactions between pairs of proteins. The challenge now is to identify novel and meaningful protein complexes from the weighted PPI network. To address this problem, a novel protein complex mining algorithm ClusterBFS (Cluster with Breadth-First Search) is proposed. Based on the weighted density, ClusterBFS detects protein complexes of the weighted network by the breadth first search algorithm, which originates from a given seed protein used as starting-point. The experimental results show that ClusterBFS performs significantly better than the other computational approaches in terms of the identification of protein complexes.
authors.affiliation: School of Information Science and Engineering, Central South University, Changsha 410083, China ; School of Information Science and Engineering, Hunan First Normal University, Changsha 410205, China.
authors.forename: Xiwei
authors.initials: X
authors.lastname: Tang
authors.affiliation: School of Information Science and Engineering, Central South University, Changsha 410083, China.
authors.forename: Jianxin
authors.initials: J
authors.lastname: Wang
authors.affiliation: School of Information Science and Engineering, Central South University, Changsha 410083, China.
authors.forename: Min
authors.initials: M
authors.lastname: Li
authors.affiliation: School of Information Science and Engineering, Central South University, Changsha 410083, China.
authors.forename: Yiming
authors.initials: Y
authors.lastname: He
authors.affiliation: School of Information Science and Engineering, Central South University, Changsha 410083, China ; Department of Computer Science, Georgia State University, Atlanta, GA 30302-4110, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Pan
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D046912:Multiprotein Complexes / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism
chemical_list: D046912:Multiprotein Complexes; D029701:Saccharomyces cerevisiae Proteins