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Volumn 5, Issue 9, 2006, Pages 2177-2184

Protein bipartivity and essentiality in the yeast protein-protein interaction network

Author keywords

Centrality measures; Essential proteins; Graph theory; Protein interactions; Protein networks; Yeast

Indexed keywords

FUNGAL PROTEIN;

EID: 33748304130     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr060106e     Document Type: Article
Times cited : (66)

References (53)
  • 1
    • 0742305866 scopus 로고    scopus 로고
    • Network biology. Understanding the cell's functional organization
    • Barabási, A.-L.; Oltvai, Z. N. Network biology. Understanding the cell's functional organization. Nat. Rev. Genet. 2004, 5, 101-113.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 101-113
    • Barabási, A.-L.1    Oltvai, Z.N.2
  • 3
    • 14844325783 scopus 로고    scopus 로고
    • From protein networks to biological systems
    • Uetz, P.; Finley, R. L, Jr. From protein networks to biological systems. FEBS Lett. 2005, 579, 1821-1827.
    • (2005) FEBS Lett. , vol.579 , pp. 1821-1827
    • Uetz, P.1    Finley Jr., R.L.2
  • 6
    • 0034659815 scopus 로고    scopus 로고
    • Proteomics to study genes and genomes
    • Pandey, A.; Mann, M. Proteomics to study genes and genomes. Nature 2000, 405, 837-846.
    • (2000) Nature , vol.405 , pp. 837-846
    • Pandey, A.1    Mann, M.2
  • 7
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • Ravasz, E.; Somera, A. L.; Mongru, D. A.; Oltvai, Z. N.; Barabási, A.-L. Hierarchical organization of modularity in metabolic networks. Science 2002, 297, 1551-1555.
    • (2002) Science , vol.297 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3    Oltvai, Z.N.4    Barabási, A.-L.5
  • 10
    • 33644644466 scopus 로고    scopus 로고
    • Identification and analysis of evolutionarily cohesive functional modules in protein networks
    • Campillos, M.; von Mering, C.; Jensen, L. J.; Bork, P. Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Res. 2006, 16, 374-382.
    • (2006) Genome Res. , vol.16 , pp. 374-382
    • Campillos, M.1    Von Mering, C.2    Jensen, L.J.3    Bork, P.4
  • 11
    • 0038699587 scopus 로고    scopus 로고
    • Global protein function prediction from protein-protein interaction networks
    • Vázquez, A.; Flammini, Á.; Maritan, Á.; Vespignani, A. Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol. 2003, 21, 697-700.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 697-700
    • Vázquez, A.1    Flammini, Á.2    Maritan, Á.3    Vespignani, A.4
  • 13
    • 0036799752 scopus 로고    scopus 로고
    • Inferring domain-domain interactions from protein-protein interactions
    • Deng, M.; Mehta, S.; Sun, F.; Chen, T. Inferring domain-domain interactions from protein-protein interactions. Genome Res. 2002, 12, 1540-1548.
    • (2002) Genome Res. , vol.12 , pp. 1540-1548
    • Deng, M.1    Mehta, S.2    Sun, F.3    Chen, T.4
  • 14
    • 0034943378 scopus 로고    scopus 로고
    • The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes
    • Wagner, A. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol. 2001, 18, 1283-1292.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1283-1292
    • Wagner, A.1
  • 15
    • 0037460091 scopus 로고    scopus 로고
    • Evolving protein interaction networks through gene duplication
    • Pastor-SaTorras, R.; Smith, E.; Sole, R. V. Evolving protein interaction networks through gene duplication. J. Theor. Biol. 2003. 222, 199-210.
    • (2003) J. Theor. Biol. , vol.222 , pp. 199-210
    • Pastor-SaTorras, R.1    Smith, E.2    Sole, R.V.3
  • 16
    • 2442631981 scopus 로고    scopus 로고
    • Convergent evolution of gene networks by single-gene duplications in higher eukariotes
    • Amoutzias, G. D.; Robertson, D. L.; Oliver, S. G.; Bornberg-Bauer, E. Convergent evolution of gene networks by single-gene duplications in higher eukariotes. EMBO Rep. 2004, 5, 1-6.
    • (2004) EMBO Rep. , vol.5 , pp. 1-6
    • Amoutzias, G.D.1    Robertson, D.L.2    Oliver, S.G.3    Bornberg-Bauer, E.4
  • 17
    • 3543099834 scopus 로고    scopus 로고
    • Evolution and topology in the yeast protein interaction network
    • Wutchy, S. Evolution and topology in the yeast protein interaction network. Genome Res. 2004, 14, 1310-1314.
    • (2004) Genome Res. , vol.14 , pp. 1310-1314
    • Wutchy, S.1
  • 18
  • 19
    • 2442477788 scopus 로고    scopus 로고
    • Genomic analysis of essentiality within protein networks
    • Yu, H.; Greenbaum, D.; Lu, H. X.; Zhu, Z.; Gerstein, M. Genomic analysis of essentiality within protein networks. Trends Genet. 2004, 20, 227-231.
    • (2004) Trends Genet. , vol.20 , pp. 227-231
    • Yu, H.1    Greenbaum, D.2    Lu, H.X.3    Zhu, Z.4    Gerstein, M.5
  • 20
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • Watts, D. J.; Strogatz, S. H. Collective dynamics of 'small-world' networks. Nature 1998, 393, 440-442.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 21
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • Barabasi, A.-L.; Albert, R. Emergence of scaling in random networks. Science 1999, 286, 509-512.
    • (1999) Science , vol.286 , pp. 509-512
    • Barabasi, A.-L.1    Albert, R.2
  • 22
    • 4644292576 scopus 로고    scopus 로고
    • The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple mode
    • van Noort, V.; Snel, B.; Huynen, M. A. The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple mode. EMBO Rep. 2004, 5, 1-5
    • (2004) EMBO Rep. , vol.5 , pp. 1-5
    • Van Noort, V.1    Snel, B.2    Huynen, M.A.3
  • 24
    • 0033565762 scopus 로고    scopus 로고
    • Do essential genes evolve slowly?
    • Hurst, L. D.; Smith, N. G. C. Do essential genes evolve slowly? Curr. Biol. 1999, 9, 747-750.
    • (1999) Curr. Biol. , vol.9 , pp. 747-750
    • Hurst, L.D.1    Smith, N.G.C.2
  • 25
    • 0035963414 scopus 로고    scopus 로고
    • Protein dispensability and rate of evolution
    • Hirsh, A. E.; Fraser, H. B. Protein dispensability and rate of evolution. Nature 2001, 411, 1046-1049.
    • (2001) Nature , vol.411 , pp. 1046-1049
    • Hirsh, A.E.1    Fraser, H.B.2
  • 26
    • 84984769114 scopus 로고    scopus 로고
    • Genomic function (communication arising): Rate of evolution and gene dispensability
    • Hirsh, A. E.; Fraser, H. B. Genomic function (communication arising): rate of evolution and gene dispensability. Nature 2003, 421, 497-498.
    • (2003) Nature , vol.421 , pp. 497-498
    • Hirsh, A.E.1    Fraser, H.B.2
  • 27
    • 0037472928 scopus 로고    scopus 로고
    • Genomic function (communication arising): Rate of evolution and gene dispensability
    • Pál, C.; Papp, B.; Hurst, L. D. Genomic function (communication arising): rate of evolution and gene dispensability. Nature 2003, 421, 496-497.
    • (2003) Nature , vol.421 , pp. 496-497
    • Pál, C.1    Papp, B.2    Hurst, L.D.3
  • 28
    • 0242380296 scopus 로고    scopus 로고
    • Conservation, relocation and duplication in genome evolution
    • Castillo-Davis, C. I.; Hard, D. L. Conservation, relocation and duplication in genome evolution. Trends Genet. 2003, 19, 593-597.
    • (2003) Trends Genet. , vol.19 , pp. 593-597
    • Castillo-Davis, C.I.1    Hard, D.L.2
  • 29
    • 2942683220 scopus 로고    scopus 로고
    • Evolution rate depends on number of protein-protein interactions independently of gene expression level: Response
    • Bloom, J. D.; Adami, C. Evolution rate depends on number of protein-protein interactions independently of gene expression level: Response. BMC Evol. Biol. 2004, 4, 14.
    • (2004) BMC Evol. Biol. , vol.4 , pp. 14
    • Bloom, J.D.1    Adami, C.2
  • 31
    • 18944391092 scopus 로고    scopus 로고
    • Biological networks and analysis of experimental data in drug discovery
    • Nikolsky, Y.; Nikolskaya, T.; Bugrim, A. Biological networks and analysis of experimental data in drug discovery. Drug Discov. Today 2005, 10, 653-662.
    • (2005) Drug Discov. Today , vol.10 , pp. 653-662
    • Nikolsky, Y.1    Nikolskaya, T.2    Bugrim, A.3
  • 32
    • 32644445902 scopus 로고    scopus 로고
    • Genomics, molecular targets and the discovery of antifungal drugs
    • Odds, F. C. Genomics, molecular targets and the discovery of antifungal drugs. Rev. Iberom. Micol. 2005, 22, 229-237.
    • (2005) Rev. Iberom. Micol. , vol.22 , pp. 229-237
    • Odds, F.C.1
  • 34
    • 0037197886 scopus 로고    scopus 로고
    • The identification of functional modules from the genomic association of genes
    • Snel, N.; Bork, P.; Huynen, M. A. The identification of functional modules from the genomic association of genes. Proc. Natl Acad. Sci. U.S.A. 2002, 99, 5890-5895.
    • (2002) Proc. Natl Acad. Sci. U.S.A. , vol.99 , pp. 5890-5895
    • Snel, N.1    Bork, P.2    Huynen, M.A.3
  • 35
    • 0037174638 scopus 로고    scopus 로고
    • Life's complexity pyramid
    • Oltvai, Z. N.; Barabási, A.-L. Life's complexity pyramid. Science 2002, 298, 763-764.
    • (2002) Science , vol.298 , pp. 763-764
    • Oltvai, Z.N.1    Barabási, A.-L.2
  • 36
    • 31344478575 scopus 로고    scopus 로고
    • Virtual identification of essential proteins within the protein interaction network of yeast
    • Estrada, E. Virtual identification of essential proteins within the protein interaction network of yeast. Proteomics 2006, 6, 35-40.
    • (2006) Proteomics , vol.6 , pp. 35-40
    • Estrada, E.1
  • 38
    • 33244461772 scopus 로고    scopus 로고
    • Spectral measures of bipartivity in complex networks
    • Estrada, E.; Rodriguez-Velazquez, J. A. Spectral measures of bipartivity in complex networks. Phys. Rev. E. 2005, 72, 046105.
    • (2005) Phys. Rev. E , vol.72 , pp. 046105
    • Estrada, E.1    Rodriguez-Velazquez, J.A.2
  • 40
    • 33750177351 scopus 로고
    • Centrality in social networks, I. Conceptual clarification
    • Freeman, L. C. Centrality in social networks, I. Conceptual clarification. Social Networks 1979, 1, 215-239.
    • (1979) Social Networks , vol.1 , pp. 215-239
    • Freeman, L.C.1
  • 41
    • 84865730611 scopus 로고
    • A set of measures of centrality based on between-ness
    • Freeman, L. C. A set of measures of centrality based on between-ness. Sociometry 1977, 40, 35-41.
    • (1977) Sociometry , vol.40 , pp. 35-41
    • Freeman, L.C.1
  • 42
    • 0001316531 scopus 로고
    • Factoring and weighting approach to clique identification
    • Bonacich, P. Factoring and weighting approach to clique identification. J. Math. Social. 1972, 2, 113-120.
    • (1972) J. Math. Social. , vol.2 , pp. 113-120
    • Bonacich, P.1
  • 43
    • 84936824655 scopus 로고
    • Power and centrality: A family of measures
    • Bonacich, P. Power and centrality: A family of measures. Am. J. Social 1987, 92, 1170-1182.
    • (1987) Am. J. Social , vol.92 , pp. 1170-1182
    • Bonacich, P.1
  • 44
    • 33645012079 scopus 로고    scopus 로고
    • Connectivity and expression in protein networks: Proteins in a complex are uniformly expressed
    • 2008
    • Carrni, S.; Levanon, E. Y.; Havlin, S.; Eisenberg, E. Connectivity and expression in protein networks: Proteins in a complex are uniformly expressed. Phys. Rev. E 2008, 031909.
    • Phys. Rev. E , pp. 031909
    • Carrni, S.1    Levanon, E.Y.2    Havlin, S.3    Eisenberg, E.4
  • 45
    • 45249126392 scopus 로고
    • Rethinking centrality: Methods and examples
    • Stephenson, K.; Zelen, M. Rethinking centrality: methods and examples. Social Networks 1989, 11, 1-37.
    • (1989) Social Networks , vol.11 , pp. 1-37
    • Stephenson, K.1    Zelen, M.2
  • 47
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering, C.; Krause, R.; Snel, B.; Cornell, M.; Oliver, S. G.; Field, S.; Bork. P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417, 399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • Von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Field, S.6    Bork, P.7
  • 50
    • 0141484611 scopus 로고    scopus 로고
    • Evolutionary conservation of motifs constituents in the yeast protein interaction network
    • Wutchy, S.; Oltvai, Z. N.; Barabasi, A.-L. Evolutionary conservation of motifs constituents in the yeast protein interaction network. Nat. Genet. 2003, 35, 176-179.
    • (2003) Nat. Genet. , vol.35 , pp. 176-179
    • Wutchy, S.1    Oltvai, Z.N.2    Barabasi, A.-L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.