title: C-element: a new clustering algorithm to find high quality functional modules in PPI networks.
abstract: Graph clustering algorithms are widely used in the analysis of biological networks. Extracting functional modules in protein-protein interaction (PPI) networks is one such use. Most clustering algorithms whose focuses are on finding functional modules try either to find a clique like sub networks or to grow clusters starting from vertices with high degrees as seeds. These algorithms do not make any difference between a biological network and any other networks. In the current research, we present a new procedure to find functional modules in PPI networks. Our main idea is to model a biological concept and to use this concept for finding good functional modules in PPI networks. In order to evaluate the quality of the obtained clusters, we compared the results of our algorithm with those of some other widely used clustering algorithms on three high throughput PPI networks from Sacchromyces Cerevisiae, Homo sapiens and Caenorhabditis elegans as well as on some tissue specific networks. Gene Ontology (GO) analyses were used to compare the results of different algorithms. Each algorithm's result was then compared with GO-term derived functional modules. We also analyzed the effect of using tissue specific networks on the quality of the obtained clusters. The experimental results indicate that the new algorithm outperforms most of the others, and this improvement is more significant when tissue specific networks are used.
authors.affiliation: Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran ; Database Research Group (DBRG), Control and Intelligent Processing Center of Excellence (CIPCE), School of Electrical and Computer Engineering, College of Engineering, University of Tehran, Tehran, Iran.
authors.forename: Mahdieh
authors.initials: M
authors.lastname: Ghasemi
authors.forename: Maseud
authors.initials: M
authors.lastname: Rahgozar
authors.forename: Gholamreza
authors.initials: G
authors.lastname: Bidkhori
authors.forename: Ali
authors.initials: A
authors.lastname: Masoudi-Nejad
mesh_terms: D000465:Algorithms; D029742:Caenorhabditis elegans Proteins / Q000502:physiology; D016000:Cluster Analysis; D019295:Computational Biology; D003198:Computer Simulation; D063990:Gene Ontology; D006801:Humans; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps; D029701:Saccharomyces cerevisiae Proteins / Q000502:physiology
chemical_list: D029742:Caenorhabditis elegans Proteins; D029701:Saccharomyces cerevisiae Proteins
references.citation: Nature. 1998 Jun 4;393(6684):440-2
references.pmid: 9623998
references.citation: Nature. 2005 Jun 9;435(7043):814-8
references.pmid: 15944704
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: PLoS Comput Biol. 2012;8(9):e1002690
references.pmid: 23028288
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Feb;69(2 Pt 2):026113
references.pmid: 14995526
references.citation: Proc Natl Acad Sci U S A. 2007 Jan 2;104(1):36-41
references.pmid: 17190818
references.citation: Nature. 1999 Dec 2;402(6761 Suppl):C47-52
references.pmid: 10591225
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D744-9
references.pmid: 20947562
references.citation: Proteins. 2004 Jan 1;54(1):49-57
references.pmid: 14705023
references.citation: Nucleic Acids Res. 2002 Apr 1;30(7):1575-84
references.pmid: 11917018
references.citation: PLoS One. 2010 Aug 16;5(8):e12200
references.pmid: 20808943
references.citation: Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12123-8
references.pmid: 14517352
references.citation: BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S61
references.pmid: 20122237
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Mar;77(3 Pt 2):036114
references.pmid: 18517468
references.citation: J Natl Cancer Inst. 1951 Jun;11(6):1269-75
references.pmid: 14861651
references.citation: BMC Bioinformatics. 2005 Apr 18;6:100
references.pmid: 15833142
references.citation: Psychometrika. 1966 Dec;31(4):581-603
references.pmid: 5232444
references.citation: Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):1128-33
references.pmid: 12538875
references.citation: Trends Biochem Sci. 2008 Dec;33(12):569-76
references.pmid: 18945619
references.citation: Bioinformatics. 2010 Apr 15;26(8):1105-11
references.pmid: 20185405
references.citation: Nat Methods. 2012 Mar 18;9(5):471-2
references.pmid: 22426491
references.citation: Bioinformatics. 2006 Apr 15;22(8):1021-3
references.pmid: 16473872
references.citation: BMC Bioinformatics. 2011 May 23;12:192
references.pmid: 21605434
references.citation: Genome Res. 2003 Nov;13(11):2498-504
references.pmid: 14597658
references.citation: Bioinformatics. 2009 Dec 1;25(23):3143-50
references.pmid: 19770263
references.citation: BMC Bioinformatics. 2003 Jan 13;4:2
references.pmid: 12525261
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Jan;77(1 Pt 2):016104
references.pmid: 18351912