title: Development and implementation of an algorithm for detection of protein complexes in large interaction networks.
abstract: BACKGROUND
  After complete sequencing of a number of genomes the focus has now turned to proteomics. Advanced proteomics technologies such as two-hybrid assay, mass spectrometry etc. are producing huge data sets of protein-protein interactions which can be portrayed as networks, and one of the burning issues is to find protein complexes in such networks. The enormous size of protein-protein interaction (PPI) networks warrants development of efficient computational methods for extraction of significant complexes.
  
  
  RESULTS
  This paper presents an algorithm for detection of protein complexes in large interaction networks. In a PPI network, a node represents a protein and an edge represents an interaction. The input to the algorithm is the associated matrix of an interaction network and the outputs are protein complexes. The complexes are determined by way of finding clusters, i. e. the densely connected regions in the network. We also show and analyze some protein complexes generated by the proposed algorithm from typical PPI networks of Escherichia coli and Saccharomyces cerevisiae. A comparison between a PPI and a random network is also performed in the context of the proposed algorithm.
  
  
  CONCLUSIONS
  The proposed algorithm makes it possible to detect clusters of proteins in PPI networks which mostly represent molecular biological functional units. Therefore, protein complexes determined solely based on interaction data can help us to predict the functions of proteins, and they are also useful to understand and explain certain biological processes.
authors.affiliation: Department of Bioinformatics and Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan. amin-m@is.naist.jp
authors.forename: Md
authors.initials: M
authors.lastname: Altaf-Ul-Amin
authors.forename: Yoko
authors.initials: Y
authors.lastname: Shinbo
authors.forename: Kenji
authors.initials: K
authors.lastname: Mihara
authors.forename: Ken
authors.initials: K
authors.lastname: Kurokawa
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Kanaya
mesh_terms: D000465:Algorithms; D002468:Cell Physiological Phenomena; D016000:Cluster Analysis; D003198:Computer Simulation; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism; D008954:Models, Biological; D010363:Pattern Recognition, Automated; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D029968:Escherichia coli Proteins; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins