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Volumn 4, Issue , 2010, Pages

The function of communities in protein interaction networks at multiple scales

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN;

EID: 77954768699     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-100     Document Type: Article
Times cited : (80)

References (65)
  • 1
    • 34047202181 scopus 로고    scopus 로고
    • Deciphering protein-protein interactions Part I Experimental techniques and databases
    • Shoemaker BA, Panchenko AR. Deciphering protein-protein interactions Part I Experimental techniques and databases. PLoS Computational Biology 2007, 3(3):337-334.
    • (2007) PLoS Computational Biology , vol.3 , Issue.3 , pp. 337-1334
    • Shoemaker, B.A.1    Panchenko, A.R.2
  • 5
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • 10.1126/science.1073374, 12202830
    • Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabási AL. Hierarchical organization of modularity in metabolic networks. Science 2002, 297(5586):1551-1555. 10.1126/science.1073374, 12202830.
    • (2002) Science , vol.297 , Issue.5586 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3    Oltvai, Z.N.4    Barabási, A.L.5
  • 7
    • 33746436302 scopus 로고    scopus 로고
    • An Introduction to Systems Biology: Design Principles of Biological Circuits
    • Chapman & Hall/CRC
    • Alon U. An Introduction to Systems Biology: Design Principles of Biological Circuits. 2007, Chapman & Hall/CRC.
    • (2007)
    • Alon, U.1
  • 8
    • 1842580761 scopus 로고    scopus 로고
    • Functional and topological characterization of protein interaction networks
    • 10.1002/pmic.200300636, 15048975
    • Yook SH, Oltvai ZN, Barabási AL. Functional and topological characterization of protein interaction networks. Proteomics 2004, 4(4):928-942. 10.1002/pmic.200300636, 15048975.
    • (2004) Proteomics , vol.4 , Issue.4 , pp. 928-942
    • Yook, S.H.1    Oltvai, Z.N.2    Barabási, A.L.3
  • 10
    • 67649866312 scopus 로고    scopus 로고
    • Structure discovery in PPI networks using pattern-based network decomposition
    • 10.1093/bioinformatics/btp297, 19447784
    • Bachman P, Liu Y. Structure discovery in PPI networks using pattern-based network decomposition. Bioinformatics 2009, 25(14):1814-1821. 10.1093/bioinformatics/btp297, 19447784.
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1814-1821
    • Bachman, P.1    Liu, Y.2
  • 12
    • 74049087026 scopus 로고    scopus 로고
    • Community detection in graphs
    • Fortunato S. Community detection in graphs. Physics Reports 2010, 486:75-174.
    • (2010) Physics Reports , vol.486 , pp. 75-174
    • Fortunato, S.1
  • 13
    • 0038074373 scopus 로고    scopus 로고
    • Topological structure analysis of the protein-protein interaction network in budding yeast
    • 10.1093/nar/gkg340, 154226, 12711690
    • Bu D, Zhao Y, Cai L, Xue H, Zhu X, Lu H, Zhang J, Sun S, Ling L, Zhang N, et al. Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Research 2003, 31(9):2443-2450. 10.1093/nar/gkg340, 154226, 12711690.
    • (2003) Nucleic Acids Research , vol.31 , Issue.9 , pp. 2443-2450
    • Bu, D.1    Zhao, Y.2    Cai, L.3    Xue, H.4    Zhu, X.5    Lu, H.6    Zhang, J.7    Sun, S.8    Ling, L.9    Zhang, N.10
  • 15
    • 25444490121 scopus 로고    scopus 로고
    • The use of edge-betweenness clustering to investigate biological function in protein interaction networks
    • 10.1186/1471-2105-6-39, 555937, 15740614
    • Dunn R, Dudbridge F, Sanderson CM. The use of edge-betweenness clustering to investigate biological function in protein interaction networks. BMC Bioinformatics 2005, 6:39. 10.1186/1471-2105-6-39, 555937, 15740614.
    • (2005) BMC Bioinformatics , vol.6 , pp. 39
    • Dunn, R.1    Dudbridge, F.2    Sanderson, C.M.3
  • 16
    • 33748701649 scopus 로고    scopus 로고
    • Detecting functional modules in the yeast protein-protein interaction network
    • 10.1093/bioinformatics/btl370, 16837529
    • Chen J, Yuan B. Detecting functional modules in the yeast protein-protein interaction network. Bioinformatics 2006, 22(18):2283-2290. 10.1093/bioinformatics/btl370, 16837529.
    • (2006) Bioinformatics , vol.22 , Issue.18 , pp. 2283-2290
    • Chen, J.1    Yuan, B.2
  • 17
    • 33846681448 scopus 로고    scopus 로고
    • Modular organization of protein interaction networks
    • 10.1093/bioinformatics/btl562, 17092991
    • Luo F, Yang Y, Chen CF, Chang R, Zhou J, Scheuermann RH. Modular organization of protein interaction networks. Bioinformatics 2007, 23(2):207-214. 10.1093/bioinformatics/btl562, 17092991.
    • (2007) Bioinformatics , vol.23 , Issue.2 , pp. 207-214
    • Luo, F.1    Yang, Y.2    Chen, C.F.3    Chang, R.4    Zhou, J.5    Scheuermann, R.H.6
  • 18
    • 49649104565 scopus 로고    scopus 로고
    • A structural approach for finding functional modules from large biological networks
    • 10.1186/1471-2105-9-S9-S19, 2537570, 18793464
    • Mete M, Tang F, Xu X, Yuruk N. A structural approach for finding functional modules from large biological networks. BMC Bioinformatics 2008, 9:S19. 10.1186/1471-2105-9-S9-S19, 2537570, 18793464.
    • (2008) BMC Bioinformatics , vol.9
    • Mete, M.1    Tang, F.2    Xu, X.3    Yuruk, N.4
  • 19
    • 50049130192 scopus 로고    scopus 로고
    • A graph-theoretic method for mining overlapping functional modules in protein interaction networks
    • Li M, Wang J, Chen J. A graph-theoretic method for mining overlapping functional modules in protein interaction networks. Lecture Notes in Bioinformatics 2008, 4983:208-219.
    • (2008) Lecture Notes in Bioinformatics , vol.4983 , pp. 208-219
    • Li, M.1    Wang, J.2    Chen, J.3
  • 23
    • 33746227724 scopus 로고    scopus 로고
    • Statistical mechanics of community detection
    • Reichardt J, Bornholdt S. Statistical mechanics of community detection. Physical Review E 2006, 74:16110.
    • (2006) Physical Review E , vol.74 , pp. 16110
    • Reichardt, J.1    Bornholdt, S.2
  • 24
    • 34848909054 scopus 로고    scopus 로고
    • Limited resolution and multiresolution methods in complex network community detection
    • Kumpula JM, Saramäki J, Kaski K, Kertész J. Limited resolution and multiresolution methods in complex network community detection. Fluctuation and Noise Letters 2007, 7(3):L209-L214.
    • (2007) Fluctuation and Noise Letters , vol.7 , Issue.3
    • Kumpula, J.M.1    Saramäki, J.2    Kaski, K.3    Kertész, J.4
  • 27
    • 46749146824 scopus 로고    scopus 로고
    • Analysis of the structure of complex networks at different resolution levels
    • Arenas A, Fernández A, Gómez S. Analysis of the structure of complex networks at different resolution levels. New Journal of Physics 2008, 10:053039.
    • (2008) New Journal of Physics , vol.10 , pp. 053039
    • Arenas, A.1    Fernández, A.2    Gómez, S.3
  • 28
    • 64549145094 scopus 로고    scopus 로고
    • Detecting the overlapping and hierarchical community structure in complex networks
    • Lancichinetti A, Fortunato S, Kertész J. Detecting the overlapping and hierarchical community structure in complex networks. New Journal of Physics 2009, 11(3):033015.
    • (2009) New Journal of Physics , vol.11 , Issue.3 , pp. 033015
    • Lancichinetti, A.1    Fortunato, S.2    Kertész, J.3
  • 29
    • 68949120793 scopus 로고    scopus 로고
    • Multiresolution community detection for megascale networks by information-based replica correlations
    • Ronhovde P, Nussinov Z. Multiresolution community detection for megascale networks by information-based replica correlations. Phys Rev E 2009, 80:016109.
    • (2009) Phys Rev E , vol.80 , pp. 016109
    • Ronhovde, P.1    Nussinov, Z.2
  • 30
    • 33947730844 scopus 로고    scopus 로고
    • Identifying functional modules in the physical interactome of Saccharomyces cerevisiae
    • 10.1002/pmic.200600636, 17370254
    • Pu S, Vlasblom J, Emili A, Greenblatt J, Wodak SJ. Identifying functional modules in the physical interactome of Saccharomyces cerevisiae. Proteomics 2007, 7(6):944-960. 10.1002/pmic.200600636, 17370254.
    • (2007) Proteomics , vol.7 , Issue.6 , pp. 944-960
    • Pu, S.1    Vlasblom, J.2    Emili, A.3    Greenblatt, J.4    Wodak, S.J.5
  • 31
    • 75949120438 scopus 로고    scopus 로고
    • How and when should interactome-derived clusters be used to predict functional modules and protein function?
    • 10.1093/bioinformatics/btp551, 19770263
    • Song J, Singh M. How and when should interactome-derived clusters be used to predict functional modules and protein function?. Bioinformatics 2009, 25(23):3143-3150. 10.1093/bioinformatics/btp551, 19770263.
    • (2009) Bioinformatics , vol.25 , Issue.23 , pp. 3143-3150
    • Song, J.1    Singh, M.2
  • 35
    • 49549092476 scopus 로고    scopus 로고
    • Mapping multiprotein complexes by affinity purification and mass spectrometry
    • 10.1016/j.copbio.2008.06.002, 18598764
    • Collins MO, Choudhary JS. Mapping multiprotein complexes by affinity purification and mass spectrometry. Current Opinion in Biotechnology 2008, 19(4):324-330. 10.1016/j.copbio.2008.06.002, 18598764.
    • (2008) Current Opinion in Biotechnology , vol.19 , Issue.4 , pp. 324-330
    • Collins, M.O.1    Choudhary, J.S.2
  • 36
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • 10.1038/nature750, 12000970
    • von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417(6887):399-403. 10.1038/nature750, 12000970.
    • (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
  • 41
    • 33748773043 scopus 로고    scopus 로고
    • Community detection as an inference problem
    • Hastings MB. Community detection as an inference problem. Physical Review E 2006, 74(3):35102.
    • (2006) Physical Review E , vol.74 , Issue.3 , pp. 35102
    • Hastings, M.B.1
  • 44
    • 71849108522 scopus 로고    scopus 로고
    • Community detection algorithms: a comparative analysis
    • Lancichinetti A, Fortunato S. Community detection algorithms: a comparative analysis. Physical Review E 2009, 80:056117.
    • (2009) Physical Review E , vol.80 , pp. 056117
    • Lancichinetti, A.1    Fortunato, S.2
  • 45
    • 77951138987 scopus 로고    scopus 로고
    • Performance of modularity maximization in practical contexts
    • Good BH, de Montjoye YA, Clauset A. Performance of modularity maximization in practical contexts. Phys Rev E 2010, 81(4):046106.
    • (2010) Phys Rev E , vol.81 , Issue.4 , pp. 046106
    • Good, B.H.1    de Montjoye, Y.A.2    Clauset, A.3
  • 46
    • 33749468596 scopus 로고    scopus 로고
    • Finding community structure in networks using the eigenvectors of matrices
    • Newman MEJ. Finding community structure in networks using the eigenvectors of matrices. Physical Review E 2006, 74(3):36104.
    • (2006) Physical Review E , vol.74 , Issue.3 , pp. 36104
    • Newman, M.E.J.1
  • 47
    • 34247223815 scopus 로고    scopus 로고
    • Quantifying social group evolution
    • 10.1038/nature05670, 17410175
    • Palla G, Barabási AL, Vicsek T. Quantifying social group evolution. Nature 2007, 446(7136):664-667. 10.1038/nature05670, 17410175.
    • (2007) Nature , vol.446 , Issue.7136 , pp. 664-667
    • Palla, G.1    Barabási, A.L.2    Vicsek, T.3
  • 48
    • 49549101132 scopus 로고    scopus 로고
    • Functional coherence in domain interaction networks
    • 10.1093/bioinformatics/btn296, 18689835
    • Pandey J, Koyuturk M, Subramaniam S, et al. Functional coherence in domain interaction networks. Bioinformatics 2008, 24:I28-I34. 10.1093/bioinformatics/btn296, 18689835.
    • (2008) Bioinformatics , vol.24
    • Pandey, J.1    Koyuturk, M.2    Subramaniam, S.3
  • 49
    • 12344269924 scopus 로고    scopus 로고
    • GO: TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    • 10.1093/bioinformatics/bth456, 15297299
    • Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G. GO: TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 2004, 20(18):3710. 10.1093/bioinformatics/bth456, 15297299.
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3710
    • Boyle, E.I.1    Weng, S.2    Gollub, J.3    Jin, H.4    Botstein, D.5    Cherry, J.M.6    Sherlock, G.7
  • 50
    • 49749109042 scopus 로고    scopus 로고
    • Introduction to Probability and Statistics
    • Brooks/Cole
    • Mendenhall W, Beaver RJ, Beaver BM. Introduction to Probability and Statistics. 2008, Brooks/Cole.
    • (2008)
    • Mendenhall, W.1    Beaver, R.J.2    Beaver, B.M.3
  • 52
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • Fawcett T. An introduction to ROC analysis. Pattern Recognition Letters 2006, 27(8):861-874.
    • (2006) Pattern Recognition Letters , vol.27 , Issue.8 , pp. 861-874
    • Fawcett, T.1
  • 53
    • 76749084811 scopus 로고    scopus 로고
    • Protein Interaction Networks - More than mere modules
    • 10.1371/journal.pcbi.1000659, 2813263, 20126533
    • Pinkert S, Schultz J, Reichardt J. Protein Interaction Networks - More than mere modules. PLoS Computational Biology 2010, 6:e1000659. 10.1371/journal.pcbi.1000659, 2813263, 20126533.
    • (2010) PLoS Computational Biology , vol.6
    • Pinkert, S.1    Schultz, J.2    Reichardt, J.3
  • 54
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world'networks
    • 10.1038/30918, 9623998
    • Watts DJ, Strogatz SH. Collective dynamics of 'small-world'networks. Nature 1998, 393(6684):440-442. 10.1038/30918, 9623998.
    • (1998) Nature , vol.393 , Issue.6684 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 55
    • 0038718854 scopus 로고    scopus 로고
    • The structure and function of complex networks
    • Newman MEJ. The structure and function of complex networks. SIAM Review 2003, 45:167-256.
    • (2003) SIAM Review , vol.45 , pp. 167-256
    • Newman, M.E.J.1
  • 56
    • 0036789265 scopus 로고    scopus 로고
    • Analyzing yeast protein-protein interaction data obtained from different sources
    • 10.1038/nbt1002-991, 12355115
    • Bader GD, Hogue CW. Analyzing yeast protein-protein interaction data obtained from different sources. Nature Biotechnology 2002, 20(10):991-997. 10.1038/nbt1002-991, 12355115.
    • (2002) Nature Biotechnology , vol.20 , Issue.10 , pp. 991-997
    • Bader, G.D.1    Hogue, C.W.2
  • 57
    • 0024640140 scopus 로고
    • An algorithm for drawing general undirected graphs
    • Kamada T, Kawai S. An algorithm for drawing general undirected graphs. Information processing letters 1989, 31:7-15.
    • (1989) Information processing letters , vol.31 , pp. 7-15
    • Kamada, T.1    Kawai, S.2
  • 58
    • 18744389789 scopus 로고    scopus 로고
    • Assortative mixing in networks
    • 10.1103/PhysRevLett.89.208701, 12443515
    • Newman MEJ. Assortative mixing in networks. Physical Review Letters 2002, 89(20):208701. 10.1103/PhysRevLett.89.208701, 12443515.
    • (2002) Physical Review Letters , vol.89 , Issue.20 , pp. 208701
    • Newman, M.E.J.1
  • 60
    • 26944456272 scopus 로고    scopus 로고
    • Network clustering coefficient without degree-correlation biases
    • Soffer SN, Vázquez A. Network clustering coefficient without degree-correlation biases. Physical Review E 2005, 71(5):57101.
    • (2005) Physical Review E , vol.71 , Issue.5 , pp. 57101
    • Soffer, S.N.1    Vázquez, A.2
  • 61
    • 0003948494 scopus 로고
    • Social Network Analysis: Methods and Applications
    • Cambridge, Cambridge University Press
    • Wasserman S, Faust K. Social Network Analysis: Methods and Applications. 1994, Cambridge, Cambridge University Press.
    • (1994)
    • Wasserman, S.1    Faust, K.2
  • 63
    • 35348957264 scopus 로고    scopus 로고
    • Efficient behavior of small-world networks
    • 10.1103/PhysRevLett.87.198701, 11690461
    • Latora V, Marchiori M. Efficient behavior of small-world networks. Physical Review Letters 2001, 87(19):198701. 10.1103/PhysRevLett.87.198701, 11690461.
    • (2001) Physical Review Letters , vol.87 , Issue.19 , pp. 198701
    • Latora, V.1    Marchiori, M.2
  • 64
    • 84976688444 scopus 로고
    • An algorithm to enumerate all cutsets of a graph in linear time per cutset
    • Tsukiyama S, Shirakawa I, Ozaki H, Ariyoshi H. An algorithm to enumerate all cutsets of a graph in linear time per cutset. Journal of the ACM 1980, 27(4):619-632.
    • (1980) Journal of the ACM , vol.27 , Issue.4 , pp. 619-632
    • Tsukiyama, S.1    Shirakawa, I.2    Ozaki, H.3    Ariyoshi, H.4


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