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Volumn 8, Issue 3, 2011, Pages 607-620

A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks

Author keywords

functional module; Gene Ontology; hierarchical clustering algorithm; Protein interaction network

Indexed keywords

BIOLOGICAL PROCESS; CELLULAR COMPONENTS; CELLULAR ORGANIZATION; COMPETING ALGORITHMS; DATA SETS; EDGE CLUSTERING; FALSE POSITIVE; FUNCTIONAL MODULES; GENE ONTOLOGY; HIERARCHICAL CLUSTERING ALGORITHMS; HIERARCHICAL ORGANIZATIONS; HIERARCHICAL STRUCTURES; HIGH THROUGHPUT EXPERIMENTS; LOW DENSITY; MOLECULAR FUNCTION; PROTEIN INTERACTION; PROTEIN INTERACTION NETWORK; PROTEIN INTERACTION NETWORKS; WEIGHTED NETWORKS; YEAST PROTEINS;

EID: 79952841798     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2010.75     Document Type: Article
Times cited : (191)

References (51)
  • 2
    • 67650160441 scopus 로고    scopus 로고
    • Hierarchical organization of functional modules in weighted protein interaction networks using clustering coefficient
    • May
    • M. Li, J. X. Wang, J. E. Chen, and Y. Pan, "Hierarchical Organization of Functional Modules in Weighted Protein Interaction Networks Using Clustering Coefficient, " Proc. Int'l Symp. Bioinformatics Research and Applications (ISBRA), pp. 75-86, May 2009.
    • (2009) Proc. Int'l Symp. Bioinformatics Research and Applications (ISBRA) , pp. 75-86
    • Li, M.1    Wang, J.X.2    Chen, J.E.3    Pan, Y.4
  • 3
    • 13244292287 scopus 로고    scopus 로고
    • Clustering proteins from interaction networks for the prediction of cellular functions
    • article
    • C. Brun, C. Herrmann, and A. Guénoche, "Clustering Proteins from Interaction Networks for the Prediction of Cellular Functions, " BMC Bioinformatcis, vol. 7, article no. 488, 2004.
    • (2004) BMC Bioinformatcis , vol.7 , Issue.488
    • Brun, C.1    Herrmann, C.2    Guénoche, A.3
  • 4
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • A. L. Barabasi and Z. N. Oltvai, "Network Biology: Understanding the Cell's Functional Organization, " Nature Rev. Genetics, vol. 5, pp. 101-114, 2004.
    • (2004) Nature Rev. Genetics , vol.5 , pp. 101-114
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 5
    • 0033518234 scopus 로고    scopus 로고
    • From molecular to modular cell biology
    • L. H. Hartwell et al., "From Molecular to Modular Cell Biology, " Nature, vol. 402, pp. C47-C52, 1999.
    • (1999) Nature , vol.402
    • Hartwell, L.H.1
  • 7
    • 1342330546 scopus 로고    scopus 로고
    • Functional topology in a network of protein interactions
    • DOI 10.1093/bioinformatics/btg415
    • N. Przulj and D. A. Wigle, "Functional Topology in a Network of Protein Interactions, " Bioinformatics, vol. 20, no. 3, pp. 340-348, 2004. (Pubitemid 38262765)
    • (2004) Bioinformatics , vol.20 , Issue.3 , pp. 340-348
    • Przulj, N.1    Wigle, D.A.2    Jurisica, I.3
  • 10
    • 1842580761 scopus 로고    scopus 로고
    • Functional and topological characterization of protein interaction networks
    • DOI 10.1002/pmic.200300636
    • S. Yook, Z. Oltvai, and A. L. Barabsi, "Functional and Topologies Characterization of Protein Interaction Networks, " Protenomics, vol. 4, pp. 928-942, 2004. (Pubitemid 38445953)
    • (2004) Proteomics , vol.4 , Issue.4 , pp. 928-942
    • Yook, S.-H.1    Oltvai, Z.N.2    Barabasi, A.-L.3
  • 11
    • 33947109414 scopus 로고    scopus 로고
    • A "seed-refine" algorithm for detecting protein complexes from protein interaction data
    • DOI 10.1109/TNB.2007.891900
    • P. Pei and A. Zhang, "A 'Seed-Refine' Algorithm for Detecting Protein Complexes from Protein Interaction Data, " IEEE Trans. Nanobioscience, vol. 6, no. 1, pp. 43-50, Mar. 2007. (Pubitemid 46397111)
    • (2007) IEEE Transactions on Nanobioscience , vol.6 , Issue.1 , pp. 43-50
    • Pei, P.1    Zhang, A.2
  • 12
    • 33751192668 scopus 로고    scopus 로고
    • Effective pre-processing strategies for functional clustering of a protein-protein interactions network
    • DOI 10.1109/BIBE.2005.25, 1544458, Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering
    • D. Ucar, S. Parthasarathy, S. Asur, and S. Chao, "Effective Preprocessing Strategies for Funcitonal Clustering of a Protein-Protein Interactions Network, " Proc. Int'l Symp. Bioinformatics and Bioeng. (BIBE), pp. 129-136, Oct. 2005. (Pubitemid 44773498)
    • (2005) Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering , vol.2005 , pp. 129-136
    • Ucar, D.1    Parthasarathy, S.2    Asur, S.3    Chao, W.4
  • 14
    • 33748579201 scopus 로고    scopus 로고
    • Interaction graph mining for protein complexes using local clique merging
    • X. L. Li, S. Tan, C. Foo, and S. Ng, "Interaction Graph Mining for Protein Complexes Using Local Clique Merging, " Genome Informatics, vol. 16, pp. 260-269, 2006.
    • (2006) Genome Informatics , vol.16 , pp. 260-269
    • Li, X.L.1    Tan, S.2    Foo, C.3    Ng, S.4
  • 15
  • 16
    • 20444504323 scopus 로고    scopus 로고
    • Uncovering the overlapping community structure of complex networks in nature and society
    • DOI 10.1038/nature03607
    • G. Palla et al., "Uncovering the Overlapping Community Structure of Complex Networks in Nature and Society, " Nature, vol. 435, no. 7043, pp. 814-818, 2005. (Pubitemid 40839731)
    • (2005) Nature , vol.435 , Issue.7043 , pp. 814-818
    • Palla, G.1    Derenyi, I.2    Farkas, I.3    Vicsek, T.4
  • 17
    • 33645830948 scopus 로고    scopus 로고
    • CFinder: Locating cliques and overlapping modules in biological networks
    • B. Adamcsek et al., "CFinder: Locating Cliques and Overlapping Modules in Biological Networks, " Bioinformatics, vol. 22, no. 8, pp. 1021-1023, 2006.
    • (2006) Bioinformatics , vol.22 , Issue.8 , pp. 1021-1023
    • Adamcsek, B.1
  • 18
    • 33744805096 scopus 로고    scopus 로고
    • Development and implementation of an algorithm for detection of protein complexes in large interaction networks
    • article
    • M. Altaf-UI-Amin et al., "Development and Implementation of an Algorithm for Detection of Protein Complexes in Large Interaction Networks, " BMC Bioinformatics, vol. 7, article no. 207, 2006.
    • (2006) BMC Bioinformatics , vol.7 , Issue.207
    • Altaf-Ui-Amin, M.1
  • 19
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • article
    • G. D. Bader and C. W. Hogue, "An Automated Method for Finding Molecular Complexes in Large Protein Interaction Networks, " BMC Bioinformatics, vol. 4, article no. 2, 2003.
    • (2003) BMC Bioinformatics , vol.4 , Issue.2
    • Bader, G.D.1    Hogue, C.W.2
  • 20
    • 10244264813 scopus 로고    scopus 로고
    • Protein complex prediction via cost-based clustering
    • DOI 10.1093/bioinformatics/bth351
    • A. D. King, N. Przulj, and I. Jurisica, "Protein Complex Prediction via Cost-Based Clustering, " Bioinformatics, vol. 20, no. 17, pp. 3013-3020, 2004. (Pubitemid 39619193)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3013-3020
    • King, A.D.1    Przulj, N.2    Jurisica, I.3
  • 22
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • DOI 10.1126/science.1073374
    • E. Ravasz et al., "Hierarchical Organization of Modularity in Metaboli Networks, " Science, vol. 297, pp. 1551-1555, 2002. (Pubitemid 34971002)
    • (2002) Science , vol.297 , Issue.5586 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3    Oltvai, Z.N.4    Barabasi, A.-L.5
  • 23
    • 40449109730 scopus 로고    scopus 로고
    • Consistent dissection of the protein interaction network by combining global and local metrics
    • article no. R271
    • C. Wang, C. Ding, Q. Yang, and S. R. Holbrook, "Consistent Dissection of the Protein Interaction Network by Combining Global and Local Metrics, " Genome Biology, vol. 8, no. 12, article no. R271, 2007.
    • (2007) Genome Biology , vol.8 , Issue.12
    • Wang, C.1    Ding, C.2    Yang, Q.3    Holbrook, S.R.4
  • 24
    • 0034515528 scopus 로고    scopus 로고
    • Clustering algorithm based on graph connectivity
    • DOI 10.1016/S0020-0190(00)00142-3
    • E. Hartuv and R. Shamir, "A Clustering Algorithm Based Graph Connectivity, " Information Processing Letters, vol. 76, nos. 4-6, pp. 175-181, 2000. (Pubitemid 32035371)
    • (2000) Information Processing Letters , vol.76 , Issue.4-6 , pp. 175-181
    • Hartuv, E.1    Shamir, R.2
  • 25
    • 0003200192 scopus 로고
    • Computers and intractability: A guide to the theory of NP-completeness
    • M. Garey and D. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness. Freeman, 1979.
    • (1979) Freeman
    • Garey, M.1    Johnson, D.2
  • 27
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • C. von Mering et al., "Comparative Assessment of Large-Scale Data Sets of Protein-Protein Interactions, " Nature, vol. 417, no. 6887, pp. 399-403, 2002. (Pubitemid 34563526)
    • (2002) Nature , vol.417 , Issue.6887 , pp. 399-403
    • Von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 28
    • 33751255087 scopus 로고    scopus 로고
    • Evaluation of clustering algorithms for protein-protein interaction networks
    • article
    • S. Brohee and J. van Helden, "Evaluation of Clustering Algorithms for Protein-Protein Interaction Networks, " BMC Bioinformatics, vol. 7, article no. 488, 2006.
    • (2006) BMC Bioinformatics , vol.7 , Issue.488
    • Brohee, S.1    Van Helden, J.2
  • 29
    • 34548511546 scopus 로고    scopus 로고
    • Semantic integration to identify overlapping functional modules in protein interaction networks
    • article
    • Y. R. Cho, W. Hwang, and M. Ramanmathan et al., "Semantic Integration to Identify Overlapping Functional Modules in Protein Interaction Networks, " BMC Bioinformatics, vol. 8, article no. 265, 2007.
    • (2007) BMC Bioinformatics , vol.8 , Issue.265
    • Cho, Y.R.1    Hwang, W.2    Ramanmathan, M.3
  • 30
    • 33845955474 scopus 로고    scopus 로고
    • Inferring topology from clustering coefficients in protein-protein interaction networks
    • article
    • C. Friedel and R. Zimmer, "Inferring Topology from Clustering Coefficients in Protein-Protein Interaction Networks, " BMC Bioinformatics, vol. 7, article no. 519, 2006.
    • (2006) BMC Bioinformatics , vol.7 , Issue.519
    • Friedel, C.1    Zimmer, R.2
  • 31
    • 0034609791 scopus 로고    scopus 로고
    • The large-scale organization of metabolic networks
    • H. Jeong et al., "The Large-Scale Organization of Metabolic Networks, " Nature, vol. 407, pp. 651-654, 2000.
    • (2000) Nature , vol.407 , pp. 651-654
    • Jeong, H.1
  • 32
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • DOI 10.1038/35075138
    • H. Jeong et al., "Lethality and Centrality in Protein Networks, " Nature, vol. 411, pp. 41-42, 2001. (Pubitemid 32428180)
    • (2001) Nature , vol.411 , Issue.6833 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.-L.3    Oltvai, Z.N.4
  • 33
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions
    • I. Xenarios et al., "DIP: The Database of Interaction Proteins: A Research Tool for Studying Cellular Networks of Protien Interactions, " Nucleic Acids Research, vol. 30, pp. 303-305, 2002. (Pubitemid 34679570)
    • (2002) Nucleic Acids Research , vol.30 , Issue.1 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.J.3    Higney, P.4    Kim, S.-M.5    Eisenberg, D.6
  • 35
    • 33646347364 scopus 로고    scopus 로고
    • Qpath: A method for querying pathways in a protein-protein interaction network
    • article
    • T. Shlomi, D. Segal, E. Ruppin, and R. Sharan, "Qpath: A Method for Querying Pathways in a Protein-Protein Interaction Network, " BMC Bioinformatics, vol. 7, article no. 199, 2006.
    • (2006) BMC Bioinformatics , vol.7 , Issue.199
    • Shlomi, T.1    Segal, D.2    Ruppin, E.3    Sharan, R.4
  • 36
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • A. C. Gavin et al., "Proteome Survey Reveals Modularity of the Yeast Cell Machinery, " Nature, vol. 440, no. 7084, pp. 631-636, 2006.
    • (2006) Nature , vol.440 , Issue.7084 , pp. 631-636
    • Gavin, A.C.1
  • 37
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast saccharomyces cerevisiae
    • N. J. Krogan et al., "Global Landscape of Protein Complexes in the Yeast Saccharomyces Cerevisiae, " Nature, vol. 440, no. 7084, pp. 637-643, 2006.
    • (2006) Nature , vol.440 , Issue.7084 , pp. 637-643
    • Krogan, N.J.1
  • 39
    • 34248397539 scopus 로고    scopus 로고
    • A novel functional module detection algorithm for protein-protein interaction networks
    • W. Hwang, Y. R. Cho, A. Zhang, and M. Ramanathan, "A Novel Functional Module Detection Algorithm for Protein-Protein Interaction Networks, " Algorithms for Molecular Biology, vol. 12, pp. 1-24, 2006.
    • (2006) Algorithms for Molecular Biology , vol.12 , pp. 1-24
    • Hwang, W.1    Cho, Y.R.2    Zhang, A.3    Ramanathan, M.4
  • 41
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • A. J. Enright, S. Van Dongen, and C. A. Ouzounis, "An Efficient Algorithm for Large-Scale Detection of Protein Families, " Nucleic Acids Research, vol. 30, no. 7, pp. 1575-1584, 2002. (Pubitemid 34679732)
    • (2002) Nucleic Acids Research , vol.30 , Issue.7 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 42
    • 65849100458 scopus 로고    scopus 로고
    • Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
    • article
    • J. Vlasblom and S. J. Wodak, "Markov Clustering versus Affinity Propagation for the Partitioning of Protein Interaction Graphs, " BMC Bioinformatics, vol. 10, article no. 99, 2009.
    • (2009) BMC Bioinformatics , vol.10 , Issue.99
    • Vlasblom, J.1    Wodak, S.J.2
  • 43
    • 67650735594 scopus 로고    scopus 로고
    • Complex discovery from weighted PPI networks
    • Aug.
    • Liu et al., "Complex Discovery from Weighted PPI Networks, " Bioinformatics, vol. 25, no. 15, pp. 1891-1897, Aug. 2009.
    • (2009) Bioinformatics , vol.25 , Issue.15 , pp. 1891-1897
    • Liu1
  • 44
    • 59649099220 scopus 로고    scopus 로고
    • Predicting protein complexes from PPI data: A core-attachment approach
    • Leung et al., "Predicting Protein Complexes from PPI Data: A Core-Attachment Approach, " J. Computational Biology, vol. 2, no. 16, pp. 133-144, 2009.
    • (2009) J. Computational Biology , vol.2 , Issue.16 , pp. 133-144
    • Leung1
  • 45
    • 79952832607 scopus 로고    scopus 로고
    • 2006
    • ftp://ftpmips.gsf.de/yeast/PPI, 2006.
  • 46
    • 79952821800 scopus 로고    scopus 로고
    • 2006
    • ftp://ftpmips.gsf.de/yeast/catalogues/complexcat/, 2006.
  • 47
    • 54349096842 scopus 로고    scopus 로고
    • Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
    • article
    • M. Li, J. Chen, J. Wang, B. Hu, and G. Chen, "Modifying the DPClus Algorithm for Identifying Protein Complexes Based on New Topological Structures, " BMC Bioinformatics, vol. 9, article no. 398, 2008.
    • (2008) BMC Bioinformatics , vol.9 , Issue.398
    • Li, M.1    Chen, J.2    Wang, J.3    Hu, B.4    Chen, G.5
  • 48
    • 0031823307 scopus 로고    scopus 로고
    • A membrane coat complex essential for endosome-to-Golgi retrograde transport in yeast
    • DOI 10.1083/jcb.142.3.665
    • M. N. Seaman et al., "A Membrane Coat Complex Essential for Endosome-to-Golgi Retrograde Transport in Yeast, " The J. Cell Biology, vol. 142, no. 3, pp. 665-681, 1998. (Pubitemid 28381486)
    • (1998) Journal of Cell Biology , vol.142 , Issue.3 , pp. 665-681
    • Seaman, M.N.J.1    McCaffery, J.M.2    Emr, S.D.3
  • 49
    • 0030964086 scopus 로고    scopus 로고
    • Cleavage factor II of saccharomyces cerevisiae contains homologues to subunits of the mammalian cleavage/polyadenylation specificity factor and exhibits sequence-specific, ATP-dependent interaction with precursor RNA
    • J. Zhao et al., "Cleavage Factor II of Saccharomyces Cerevisiae Contains Homologues to Subunits of the Mammalian Cleavage/Polyadenylation Specificity Factor and Exhibits Sequence-Specific, ATP-Dependent Interaction with Precursor RNA, " The J. Biological Chemistry, vol. 272, no. 16, pp. 10831-10838, 1997.
    • (1997) The J. Biological Chemistry , vol.272 , Issue.16 , pp. 10831-10838
    • Zhao, J.1
  • 50
    • 0035933149 scopus 로고    scopus 로고
    • Five subunits are required for reconstitution of the cleavage and polyadenylation activities of Saccharomyces cerevisiae cleavage factor I
    • DOI 10.1073/pnas.101046598
    • S. Gross and C. Moore, "Five Subunits are Required for Reconstitution of the Cleavage and Polyadenylation Activities of Saccharomyces Cerevisiae Cleavage Factor I, " Proc. Nat'l Academy of Sciences USA, vol. 98, no. 11, pp. 6080-6085, 2001. (Pubitemid 32488196)
    • (2001) Proceedings of the National Academy of Sciences of the United States of America , vol.98 , Issue.11 , pp. 6080-6085
    • Gross, S.1    Moore, C.2
  • 51
    • 0033622037 scopus 로고    scopus 로고
    • Identification and characterization of five new subunits of TRAPP
    • 2000
    • M. Sacher et al., "Identification and Characterization of Five New Subunits of TRAPP, " European J. Cell Biology, vol. 79, no. 2, pp. 71-80, http://netlab.csu.edu.cn/bioinformatics/limin/HC-PIN, 2000.
    • European J. Cell. Biology , vol.79 , Issue.2 , pp. 71-80
    • Sacher, M.1


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