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Volumn 6, Issue 1, 2010, Pages

Protein interaction networks-more than mere modules

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL INTELLIGENCE;

EID: 76749084811     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000659     Document Type: Article
Times cited : (51)

References (52)
  • 1
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cells's functional organization
    • Barabási AL, Oltvai Z (2004) Network biology: Understanding the cells's functional organization. Nature Reviews Genetics 5: 101-113.
    • (2004) Nature Reviews Genetics , vol.5 , pp. 101-113
    • Barabási, A.L.1    Oltvai, Z.2
  • 3
    • 0034628487 scopus 로고    scopus 로고
    • Guilt-by-association goes global
    • Oliver S (2000) Guilt-by-association goes global. Nature 403: 601-603.
    • (2000) Nature , vol.403 , pp. 601-603
    • Oliver, S.1
  • 4
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • Spirin V, Mirny L (2003) Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 100: 12123-12128.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.2
  • 5
    • 42949105070 scopus 로고    scopus 로고
    • An algorithm for finding functional modules and protein complexes in protein-protein interaction networks
    • Cui G, Chen Y, Huang D, Han K (2008) An algorithm for finding functional modules and protein complexes in protein-protein interaction networks. J Biomed Biotechnol 2008: 860270.
    • (2008) J Biomed Biotechnol 2008 , pp. 860270
    • Cui, G.1    Chen, Y.2    Huang, D.3    Han, K.4
  • 6
    • 34248397539 scopus 로고    scopus 로고
    • A novel functional module detection algorithm for protein-protein interaction networks
    • Hwang W, Cho Y, Zhang A, Ramanathan M (2006) A novel functional module detection algorithm for protein-protein interaction networks. Algorithms Mol Biol 1: 24.
    • (2006) Algorithms Mol Biol , vol.1 , pp. 24
    • Hwang, W.1    Cho, Y.2    Zhang, A.3    Ramanathan, M.4
  • 7
    • 20444504323 scopus 로고    scopus 로고
    • Uncovering the overlapping community structure of complex networks in nature and society
    • Palla G, Derenyi I, Farkas I, Vicsek T (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435: 814.
    • (2005) Nature , vol.435 , pp. 814
    • Palla, G.1    Derenyi, I.2    Farkas, I.3    Vicsek, T.4
  • 8
    • 33645830948 scopus 로고    scopus 로고
    • Cfinder: Locating cliques and overlapping modules in biological networks
    • Adamcsek B, Palla G, Farkas IJ, Derényi I, Vicsek T (2006) Cfinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22: 1021-1023.
    • (2006) Bioinformatics , vol.22 , pp. 1021-1023
    • Adamcsek, B.1    Palla, G.2    Farkas, I.J.3    Derényi, I.4    Vicsek, T.5
  • 9
    • 0038074373 scopus 로고    scopus 로고
    • Topological structure analysis of the protein-protein interaction network in budding yeast
    • Bu D, Zhao Z, Cai L, Xue H, Lu H, et al. (2003) Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res 31: 2443-2450.
    • (2003) Nucleic Acids Res , vol.31 , pp. 2443-2450
    • Bu, D.1    Zhao, Z.2    Cai, L.3    Xue, H.4    Lu, H.5
  • 10
    • 25444490121 scopus 로고    scopus 로고
    • The use of edge-betweenness clustering to investigate biological function in protein interaction networks
    • Dunn R, Dudbridge F, Sanderson CM (2005) The use of edge-betweenness clustering to investigate biological function in protein interaction networks. BMC Bioinformatics 6: 39.
    • (2005) BMC Bioinformatics , vol.6 , pp. 39
    • Dunn, R.1    Dudbridge, F.2    Sanderson, C.M.3
  • 11
    • 10244264813 scopus 로고    scopus 로고
    • Protein complex prediction via cost-based clustering
    • King AD, Przulj N, Jurisica I (2004) Protein complex prediction via cost-based clustering. Bioinformatics 20: 3013-3012.
    • (2004) Bioinformatics , vol.20 , pp. 3013-3012
    • King, A.D.1    Przulj, N.2    Jurisica, I.3
  • 12
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in yeast saccharomyces cerevisiae
    • Krognan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in yeast saccharomyces cerevisiae. Nature 440: 637-643.
    • (2006) Nature , vol.440 , pp. 637-643
    • Krognan, N.J.1    Cagney, G.2    Yu, H.3    Zhong, G.4    Guo, X.5
  • 13
    • 0346156102 scopus 로고    scopus 로고
    • Detection of functional modules from protein interaction networks
    • Pereira-Leal JB, Enright AJ, Ouzounis CA (2004) Detection of functional modules from protein interaction networks. Proteins 54: 49-57.
    • (2004) Proteins , vol.54 , pp. 49-57
    • Pereira-Leal, J.B.1    Enright, A.J.2    Ouzounis, C.A.3
  • 14
    • 1342330546 scopus 로고    scopus 로고
    • Functional topology in a network of protein interactions
    • Przulj N, Wiggle DA, Jurisica I (2004) Functional topology in a network of protein interactions. Bioinformatics 20: 340-348.
    • (2004) Bioinformatics , vol.20 , pp. 340-348
    • Przulj, N.1    Wiggle, D.A.2    Jurisica, I.3
  • 16
    • 43049151837 scopus 로고    scopus 로고
    • Clauset A, Moor C, Newman M (2008453) Hierarchical structure and the prediction of missing links in networks. Nature. pp 98-101.
    • Clauset A, Moor C, Newman M (2008453) Hierarchical structure and the prediction of missing links in networks. Nature. pp 98-101.
  • 17
    • 34347329333 scopus 로고    scopus 로고
    • In search of the biological significance of modular structures in protein networks
    • Wang Z, Zhang J (2007) In search of the biological significance of modular structures in protein networks. PLoS Comput Biol 3: e107.
    • (2007) PLoS Comput Biol , vol.3
    • Wang, Z.1    Zhang, J.2
  • 18
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin A, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.1    Aloy, P.2    Grandi, P.3    Krause, R.4    Boesche, M.5
  • 19
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • Gavin A, Bösche M, Krause R, Grandi P, Marzioch M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
    • (2002) Nature , vol.415 , pp. 141-147
    • Gavin, A.1    Bösche, M.2    Krause, R.3    Grandi, P.4    Marzioch, M.5
  • 20
    • 34247922700 scopus 로고
    • Graph and semigroup homomorphisms
    • White D, Reitz K (1983) Graph and semigroup homomorphisms. Soc Networks 5: 193-234.
    • (1983) Soc Networks , vol.5 , pp. 193-234
    • White, D.1    Reitz, K.2
  • 21
    • 0001964443 scopus 로고
    • Structural equivalence of individuals in social networks
    • Lorrain F, White H (1971) Structural equivalence of individuals in social networks. J Math Sociol 1: 49-80.
    • (1971) J Math Sociol , vol.1 , pp. 49-80
    • Lorrain, F.1    White, H.2
  • 24
    • 37649028224 scopus 로고    scopus 로고
    • Finding and evaluating community structure in networks
    • Newman MEJ, Girvan M (2004) Finding and evaluating community structure in networks. Phys Rev E 69: 026113.
    • (2004) Phys Rev E , vol.69 , pp. 026113
    • Newman, M.E.J.1    Girvan, M.2
  • 25
    • 14644396645 scopus 로고    scopus 로고
    • Functional cartography of complex metabolic networks
    • Guimerà R, Nunes Amaral L (2005) Functional cartography of complex metabolic networks. Nature 433: 895-900.
    • (2005) Nature , vol.433 , pp. 895-900
    • Guimerà, R.1    Nunes Amaral, L.2
  • 26
    • 37249033857 scopus 로고    scopus 로고
    • Role models for complex networks
    • Reichardt J, White DR (2007) Role models for complex networks. Eur Phys J B 60: 217-224.
    • (2007) Eur Phys J B , vol.60 , pp. 217-224
    • Reichardt, J.1    White, D.R.2
  • 27
    • 84869457823 scopus 로고    scopus 로고
    • Structure in Networks
    • of Springer-Verlag Berlin Heidelberg
    • Reichardt J (2008) Structure in Networks, volume 766 of Lecture Notes in Physics Springer-Verlag Berlin Heidelberg.
    • (2008) Lecture Notes in Physics , vol.766
    • Reichardt, J.1
  • 28
  • 29
    • 26444479778 scopus 로고
    • Optimization by simmulated annealing
    • Kirkpatrick S, Jr CG, Vecchi M (1983) Optimization by simmulated annealing. Science 220: 671-680.
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    CG, J.2    Vecchi, M.3
  • 30
    • 34547405111 scopus 로고    scopus 로고
    • Mixture models and exploratory data analysis in networks
    • Newman M, Leicht E (2007) Mixture models and exploratory data analysis in networks. Proc Natl Acac Sci USA 104: 9564-9569.
    • (2007) Proc Natl Acac Sci USA , vol.104 , pp. 9564-9569
    • Newman, M.1    Leicht, E.2
  • 31
    • 34250655368 scopus 로고    scopus 로고
    • An information-theoretic framework for resolving community structure in complex networks
    • Rosvall M, Bergstrom C (2007) An information-theoretic framework for resolving community structure in complex networks. Proc Natl Acac Sci USA 104: 7327-7331.
    • (2007) Proc Natl Acac Sci USA , vol.104 , pp. 7327-7331
    • Rosvall, M.1    Bergstrom, C.2
  • 32
    • 0033592606 scopus 로고    scopus 로고
    • Learning the parts of an object by nonnegative matrix factorization
    • Lee DD, Seung SH (1999) Learning the parts of an object by nonnegative matrix factorization. Nature 401: 788-791.
    • (1999) Nature , vol.401 , pp. 788-791
    • Lee, D.D.1    Seung, S.H.2
  • 35
    • 48249137780 scopus 로고    scopus 로고
    • Royer L, Reimann M, Andreopoulos B, Schroeder M (2008) Unraveleing protein networks with power graph analysis. PLoS Comput Biol 4: e1000108.
    • Royer L, Reimann M, Andreopoulos B, Schroeder M (2008) Unraveleing protein networks with power graph analysis. PLoS Comput Biol 4: e1000108.
  • 36
    • 29244482771 scopus 로고    scopus 로고
    • Genetic interaction motif finding by expectation maximization - a novel statistical model for inferring gene modules from synthetic lethality
    • Qui Y, Ye P, Bader JS (2005) Genetic interaction motif finding by expectation maximization - a novel statistical model for inferring gene modules from synthetic lethality. BMC Bioinformatics 6: 288.
    • (2005) BMC Bioinformatics , vol.6 , pp. 288
    • Qui, Y.1    Ye, P.2    Bader, J.S.3
  • 37
    • 36448946146 scopus 로고    scopus 로고
    • Improved detection of overrepresentation of gene-ontology annotations with parent-child analysis
    • Grossmann S, Bauer S, Robinson PN, Vingron M (2007) Improved detection of overrepresentation of gene-ontology annotations with parent-child analysis. Bioinformatics 23: 3024-3013.
    • (2007) Bioinformatics , vol.23 , pp. 3024-3013
    • Grossmann, S.1    Bauer, S.2    Robinson, P.N.3    Vingron, M.4
  • 38
    • 33746227724 scopus 로고    scopus 로고
    • Statistical mechanics of community detection
    • Reichardt J, Bornholdt S (2006) Statistical mechanics of community detection. Phys Rev E 74: 016110.
    • (2006) Phys Rev E , vol.74 , pp. 016110
    • Reichardt, J.1    Bornholdt, S.2
  • 39
    • 0037123605 scopus 로고    scopus 로고
    • Emerging roles of ubiquitin in transcription regulation
    • Conaway RC, Brown CS, Conaway JW (2002) Emerging roles of ubiquitin in transcription regulation. Science 296: 1254-1258.
    • (2002) Science , vol.296 , pp. 1254-1258
    • Conaway, R.C.1    Brown, C.S.2    Conaway, J.W.3
  • 41
    • 0024406857 scopus 로고
    • A novel genetic system to detect protein-protein interactions
    • Fields S, Song O (1989) A novel genetic system to detect protein-protein interactions. Nature 340: 245-246.
    • (1989) Nature , vol.340 , pp. 245-246
    • Fields, S.1    Song, O.2
  • 42
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98: 4569-4574.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 4569-4574
    • Ito, T.1    Chiba, T.2    Ozawa, R.3    Yoshida, M.4    Hattori, M.5
  • 43
    • 60849107715 scopus 로고    scopus 로고
    • A new graph-based method for pairwise global network alignment
    • Klau GW (2009) A new graph-based method for pairwise global network alignment. BMC Bioinformatics 10: 1:S59.
    • (2009) BMC Bioinformatics , vol.10 , Issue.1
    • Klau, G.W.1
  • 44
    • 51349087811 scopus 로고    scopus 로고
    • Global alignment of multiple protein interaction networks with application to functional orthology detection
    • Singh R, Xu J, Berger B (2008) Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc Natl Acac Sci USA 105: 12763-8.
    • (2008) Proc Natl Acac Sci USA , vol.105 , pp. 12763-12768
    • Singh, R.1    Xu, J.2    Berger, B.3
  • 45
    • 0034667776 scopus 로고    scopus 로고
    • A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters
    • Ogata H, Fujubuchi W, Goto S, Kanehisa M (2000) A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res 28: 4021-8.
    • (2000) Nucleic Acids Res , vol.28 , pp. 4021-4028
    • Ogata, H.1    Fujubuchi, W.2    Goto, S.3    Kanehisa, M.4
  • 46
    • 23844447959 scopus 로고    scopus 로고
    • Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
    • Sharan R, Ideker T, Kelley B, Shamir R, Karp RM (2005) Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol 12: 835-46.
    • (2005) J Comput Biol , vol.12 , pp. 835-846
    • Sharan, R.1    Ideker, T.2    Kelley, B.3    Shamir, R.4    Karp, R.M.5
  • 47
    • 49749151329 scopus 로고    scopus 로고
    • (Un)detectable cluster structure in sparse networks
    • Reichardt J, Leone M (2008) (Un)detectable cluster structure in sparse networks. Phys Rev Lett 101: 078701.
    • (2008) Phys Rev Lett , vol.101 , pp. 078701
    • Reichardt, J.1    Leone, M.2
  • 50
    • 0037012880 scopus 로고    scopus 로고
    • Specificity and stability in topology of protein networks
    • Maslov S, Sneppen K (2002) Specificity and stability in topology of protein networks. Science 296: 910-913.
    • (2002) Science , vol.296 , pp. 910-913
    • Maslov, S.1    Sneppen, K.2
  • 51
    • 47049099111 scopus 로고    scopus 로고
    • Ontologizer 2.0 - A Multifunctional Tool for GO Term Enrichment Analysis and Data Exploration
    • Bauer S, Grossmann S, Vingron M, Robinson P (2008) Ontologizer 2.0 - A Multifunctional Tool for GO Term Enrichment Analysis and Data Exploration. Bioinformatics.
    • (2008) Bioinformatics
    • Bauer, S.1    Grossmann, S.2    Vingron, M.3    Robinson, P.4
  • 52
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball C, Blake J, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.2    Blake, J.3    Botstein, D.4    Butler, H.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.