메뉴 건너뛰기




Volumn 10, Issue , 2009, Pages 333-

Phylogenetic analysis of modularity in protein interaction networks

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE ANALYSIS; EVOLUTIONARY HISTORY; FUNCTIONAL MODULARITY; KEY CHARACTERISTICS; PHYLOGENETIC ANALYSIS; PHYLOGENY RECONSTRUCTION; PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTIONS;

EID: 70450237111     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-333     Document Type: Article
Times cited : (30)

References (37)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schffer AA, J Zhang ZZ, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research 1997, 25(17):3389-340. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Research , vol.25 , Issue.17 , pp. 3389-4340
    • Altschul, S.F.1    Madden, T.L.2    Schffer, A.A.3    J Zhang, Z.Z.4    Miller, W.5    Lipman, D.J.6
  • 5
    • 13444278821 scopus 로고    scopus 로고
    • Reconstruction of cellular signalling networks and analysis of their properties
    • 10.1038/nrm1570, 15654321
    • Papin JA, Hunter T, Palsson BO, Subramaniam S. Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol 2005, 6(2):99-111. 10.1038/nrm1570, 15654321.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , Issue.2 , pp. 99-111
    • Papin, J.A.1    Hunter, T.2    Palsson, B.O.3    Subramaniam, S.4
  • 6
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: a brief overview
    • 10.1126/science.1069492, 11872829
    • Kitano H. Systems biology: a brief overview. Science 2002, 295(5560):1662-1664. 10.1126/science.1069492, 11872829.
    • (2002) Science , vol.295 , Issue.5560 , pp. 1662-1664
    • Kitano, H.1
  • 8
    • 33748257786 scopus 로고    scopus 로고
    • Graemlin: general and robust alignment of multiple large interaction networks
    • 10.1101/gr.5235706, 1557769, 16899655
    • Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S. Graemlin: general and robust alignment of multiple large interaction networks. Genome Research 2006, 16(9):1169-1181. 10.1101/gr.5235706, 1557769, 16899655.
    • (2006) Genome Research , vol.16 , Issue.9 , pp. 1169-1181
    • Flannick, J.1    Novak, A.2    Srinivasan, B.S.3    McAdams, H.H.4    Batzoglou, S.5
  • 9
    • 33846194268 scopus 로고    scopus 로고
    • Detecting conserved interaction patterns in biological networks
    • 10.1089/cmb.2006.13.1299, 17037960
    • Koyutürk M, Kim Y, Subramaniam S, Szpankowski W, Grama A. Detecting conserved interaction patterns in biological networks. Journal of Computational Biology 2006, 13(7):1299-1322. 10.1089/cmb.2006.13.1299, 17037960.
    • (2006) Journal of Computational Biology , vol.13 , Issue.7 , pp. 1299-1322
    • Koyutürk, M.1    Kim, Y.2    Subramaniam, S.3    Szpankowski, W.4    Grama, A.5
  • 10
    • 33645732240 scopus 로고    scopus 로고
    • Modeling cellular machinery through biological network comparison
    • 10.1038/nbt1196, 16601728
    • Sharan R, Ideker T. Modeling cellular machinery through biological network comparison. Nature Biotechnology 2006, 24(4):427-433. 10.1038/nbt1196, 16601728.
    • (2006) Nature Biotechnology , vol.24 , Issue.4 , pp. 427-433
    • Sharan, R.1    Ideker, T.2
  • 11
    • 0141484611 scopus 로고    scopus 로고
    • Evolutionary conservation of motif constituents in the yeast protein interaction network
    • 10.1038/ng1242, 12973352
    • Wuchty S, Oltvai ZN, Barabási AL. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nature Genetics 2003, 35(2):176-179. 10.1038/ng1242, 12973352.
    • (2003) Nature Genetics , vol.35 , Issue.2 , pp. 176-179
    • Wuchty, S.1    Oltvai, Z.N.2    Barabási, A.L.3
  • 12
    • 33644656793 scopus 로고    scopus 로고
    • Systematic identification of functional orthologs based on protein network comparison
    • 10.1101/gr.4526006, 1415213, 16510899
    • Bandyopadhyay S, Sharan R, Ideker T. Systematic identification of functional orthologs based on protein network comparison. Genome Res 2006, 16(3):428-435. 10.1101/gr.4526006, 1415213, 16510899.
    • (2006) Genome Res , vol.16 , Issue.3 , pp. 428-435
    • Bandyopadhyay, S.1    Sharan, R.2    Ideker, T.3
  • 16
    • 33745801977 scopus 로고    scopus 로고
    • Biological Networks: Comparison, Conservation, and Evolutionary Trees
    • Chor B, Tuller T. Biological Networks: Comparison, Conservation, and Evolutionary Trees. RECOMB 2006, 30-44.
    • (2006) RECOMB , pp. 30-44
    • Chor, B.1    Tuller, T.2
  • 17
    • 0141730411 scopus 로고    scopus 로고
    • Evolution thinks modular
    • 10.1038/ng1003-118, 14517536
    • Vespignani A. Evolution thinks modular. Nature Genetics 2003, 35(2):118-119. 10.1038/ng1003-118, 14517536.
    • (2003) Nature Genetics , vol.35 , Issue.2 , pp. 118-119
    • Vespignani, A.1
  • 18
    • 18244365622 scopus 로고    scopus 로고
    • Extraction of phylogenetic network modules from prokayrote metabolic pathways
    • Yamada T, Goto S, Kanehisa M. Extraction of phylogenetic network modules from prokayrote metabolic pathways. Genome Inform 2004, 15:249-258., http://view.ncbi.nlm.nih.gov/pubmed/15712127
    • (2004) Genome Inform , vol.15 , pp. 249-258
    • Yamada, T.1    Goto, S.2    Kanehisa, M.3
  • 19
    • 23744481400 scopus 로고    scopus 로고
    • What do we learn from high-throughput protein interaction data?
    • 10.1586/14789450.1.1.111, 15966804
    • Titz B, Schlesner M, Uetz P. What do we learn from high-throughput protein interaction data?. Expert Review of Proteomics 2004, 1:111-121. 10.1586/14789450.1.1.111, 15966804.
    • (2004) Expert Review of Proteomics , vol.1 , pp. 111-121
    • Titz, B.1    Schlesner, M.2    Uetz, P.3
  • 20
    • 14744273317 scopus 로고    scopus 로고
    • Inferring network mechanisms: The Drosophila melanogaster protein interaction network
    • 10.1073/pnas.0409515102
    • Middendorf M, Ziv E, Wiggins CH. Inferring network mechanisms: The Drosophila melanogaster protein interaction network. Proceedings of the National Academy of Sciences 2005, 102(9):3192-3197. 10.1073/pnas.0409515102.
    • (2005) Proceedings of the National Academy of Sciences , vol.102 , Issue.9 , pp. 3192-3197
    • Middendorf, M.1    Ziv, E.2    Wiggins, C.H.3
  • 21
    • 0037460091 scopus 로고    scopus 로고
    • Evolving protein interaction networks through gene duplication
    • 10.1016/S0022-5193(03)00028-6, 12727455
    • Pastor-Satorras R, Smith E, Sole RV. Evolving protein interaction networks through gene duplication. J Theor Biol 2003, 222(2):199-210. 10.1016/S0022-5193(03)00028-6, 12727455.
    • (2003) J Theor Biol , vol.222 , Issue.2 , pp. 199-210
    • Pastor-Satorras, R.1    Smith, E.2    Sole, R.V.3
  • 22
    • 9444239213 scopus 로고    scopus 로고
    • A probabilistic functional network of yeast genes
    • 10.1126/science.1099511, 15567862
    • Lee I, Date SV, Adai AT, Marcotte EM. A probabilistic functional network of yeast genes. Science 2004, 306(5701):1555-1558. 10.1126/science.1099511, 15567862.
    • (2004) Science , vol.306 , Issue.5701 , pp. 1555-1558
    • Lee, I.1    Date, S.V.2    Adai, A.T.3    Marcotte, E.M.4
  • 23
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • 10.1073/pnas.2032324100, 218723, 14517352
    • Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. PNAS 2003, 100(21):12123-12128. 10.1073/pnas.2032324100, 218723, 14517352.
    • (2003) PNAS , vol.100 , Issue.21 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 24
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4(2).
    • (2003) BMC Bioinformatics , vol.4 , Issue.2
    • Bader, G.D.1    Hogue, C.W.2
  • 25
    • 36849004088 scopus 로고    scopus 로고
    • PathFinder: mining signal transduction pathway segments from protein-protein interaction networks
    • 10.1186/1471-2105-8-335, 2100073, 17854489
    • Bebek G, Yang J. PathFinder: mining signal transduction pathway segments from protein-protein interaction networks. BMC Bioinformatics 2007, 8:335+. 10.1186/1471-2105-8-335, 2100073, 17854489.
    • (2007) BMC Bioinformatics , vol.8
    • Bebek, G.1    Yang, J.2
  • 27
  • 28
    • 0141593601 scopus 로고    scopus 로고
    • Conserved pathways within bacteria and yeast as revealed by global protein network alignment
    • 10.1073/pnas.1534710100, 208768, 14504397
    • Kelley BP, Sharan R, Karp RM, Sittler T, Root DE, Stockwell BR, Ideker T. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. PNAS 2003, 100(20):11394-11399. 10.1073/pnas.1534710100, 208768, 14504397.
    • (2003) PNAS , vol.100 , Issue.20 , pp. 11394-11399
    • Kelley, B.P.1    Sharan, R.2    Karp, R.M.3    Sittler, T.4    Root, D.E.5    Stockwell, B.R.6    Ideker, T.7
  • 29
    • 0037447257 scopus 로고    scopus 로고
    • Assessing experimentally derived interactions in a small world
    • Goldberg D, Roth F. Assessing experimentally derived interactions in a small world. Proceedings of the National Academy of Sciences 2003, 100(8):4372-4376.
    • (2003) Proceedings of the National Academy of Sciences , vol.100 , Issue.8 , pp. 4372-4376
    • Goldberg, D.1    Roth, F.2
  • 30
    • 0023375195 scopus 로고
    • The neighbor-joining method: a new method for reconstructing phylogenetic trees
    • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4(4):406-425.
    • (1987) Mol Biol Evol , vol.4 , Issue.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 33
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • 10.1016/0025-5564(81)90043-2
    • Robinson DF, Foulds LR. Comparison of phylogenetic trees. Mathematical Biosciences 1981, 53(1-2):131-147. 10.1016/0025-5564(81)90043-2.
    • (1981) Mathematical Biosciences , vol.53 , Issue.1-2 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 35
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
    • 10.1093/nar/30.1.303, 99070, 11752321
    • Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 2002, 30:303-305. 10.1093/nar/30.1.303, 99070, 11752321., http://dip.doe-mbi.ucla.edu
    • (2002) Nucleic Acids Res , vol.30 , pp. 303-305
    • Xenarios, I.1    Fernandez, E.2    Salwinski, L.3    Duan, X.J.4    Thompson, M.J.5    Marcotte, E.M.6    Eisenberg, D.7
  • 36
    • 33644700003 scopus 로고    scopus 로고
    • Toward Automatic Reconstruction of a Highly Resolved Tree of Life
    • 10.1126/science.1123061, 16513982
    • Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward Automatic Reconstruction of a Highly Resolved Tree of Life. Science 2006, 311(5765):1283-1287. 10.1126/science.1123061, 16513982.
    • (2006) Science , vol.311 , Issue.5765 , pp. 1283-1287
    • Ciccarelli, F.D.1    Doerks, T.2    von Mering, C.3    Creevey, C.J.4    Snel, B.5    Bork, P.6
  • 37
    • 35848952076 scopus 로고    scopus 로고
    • Support for the Coelomata Clade of Animals from a Rigorous Analysis of the Pattern of Intron Conservation
    • 10.1093/molbev/msm207, 17893400
    • Zheng J, Rogozin IB, Koonin EV, Przytycka TM. Support for the Coelomata Clade of Animals from a Rigorous Analysis of the Pattern of Intron Conservation. Molecular Biology and Evolution 2007, 24(11):2583-2592. 10.1093/molbev/msm207, 17893400.
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.11 , pp. 2583-2592
    • Zheng, J.1    Rogozin, I.B.2    Koonin, E.V.3    Przytycka, T.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.