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Volumn 4, Issue 8, 2008, Pages

Why do hubs in the yeast protein interaction network tend to be essential: Reexamining the connection between the network topology and essentiality

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINS; YEAST;

EID: 50949092459     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000140     Document Type: Article
Times cited : (354)

References (39)
  • 1
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong H, Mason SP, Barabási AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411(6833): 41-42.
    • (2001) Nature , vol.411 , Issue.6833 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabási, A.L.3    Oltvai, Z.N.4
  • 3
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong H, Mason SP, Barabási AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411(6833): 41-42.
    • (2001) Nature , vol.411 , Issue.6833 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabási, A.L.3    Oltvai, Z.N.4
  • 4
    • 33746631391 scopus 로고    scopus 로고
    • Evolutionary and physiological importance of hub proteins
    • doi:10.1371/journal. pcbi.0020088
    • Batada NN, Hurst LD, Tyers M (2006) Evolutionary and physiological importance of hub proteins. PLoS Comput Biol 2(7): e88. doi:10.1371/journal. pcbi.0020088.
    • (2006) PLoS Comput Biol , vol.2 , Issue.7
    • Batada, N.N.1    Hurst, L.D.2    Tyers, M.3
  • 5
    • 16344381521 scopus 로고    scopus 로고
    • Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
    • Hahn MW, Kern AD (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 22(4): 803-806.
    • (2005) Mol Biol Evol , vol.22 , Issue.4 , pp. 803-806
    • Hahn, M.W.1    Kern, A.D.2
  • 6
    • 2442477788 scopus 로고    scopus 로고
    • Genomic analysis of essentiality within protein networks
    • Yu H, Greenbaum D, Xin Lu H, Zhu X, Gerstein M (2004) Genomic analysis of essentiality within protein networks. Trends Genet 20(6): 227-231.
    • (2004) Trends Genet , vol.20 , Issue.6 , pp. 227-231
    • Yu, H.1    Greenbaum, D.2    Xin Lu, H.3    Zhu, X.4    Gerstein, M.5
  • 7
    • 34247622363 scopus 로고    scopus 로고
    • The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics
    • doi:10.1371/journal.pcbi. 0030059
    • Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M (2007) The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 3(4): e59. doi:10.1371/journal.pcbi. 0030059.
    • (2007) PLoS Comput Biol , vol.3 , Issue.4
    • Yu, H.1    Kim, P.M.2    Sprecher, E.3    Trifonov, V.4    Gerstein, M.5
  • 8
    • 0034721164 scopus 로고    scopus 로고
    • Error and attack tolerance of complex networks
    • Albert R, Jeong H, Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406(6794): 378-382.
    • (2000) Nature , vol.406 , Issue.6794 , pp. 378-382
    • Albert, R.1    Jeong, H.2    Barabasi, A.L.3
  • 10
    • 0036580169 scopus 로고    scopus 로고
    • Protein interactions: Two methods for assessment of the reliability of high throughput observations
    • Deane CM, Salwiński Ł, Xenarios I, Eisenberg D (2002) Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics 1(5): 349-356.
    • (2002) Mol Cell Proteomics , vol.1 , Issue.5 , pp. 349-356
    • Deane, C.M.1    Salwiński, Ł.2    Xenarios, I.3    Eisenberg, D.4
  • 11
    • 33847064282 scopus 로고    scopus 로고
    • Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
    • Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, et al. (2006) Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol 5(4): 11.
    • (2006) J Biol , vol.5 , Issue.4 , pp. 11
    • Reguly, T.1    Breitkreutz, A.2    Boucher, L.3    Breitkreutz, B.J.4    Hon, G.C.5
  • 12
    • 33750238153 scopus 로고    scopus 로고
    • Stratus not altocumulus: A new view of the yeast protein interaction network
    • doi:10.1371/journal.pbio.0040317
    • Batada NN, Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, et al. (2006) Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol 2006 4(10): e317. doi:10.1371/journal.pbio.0040317.
    • (2006) PLoS Biol , vol.4 , Issue.10
    • Batada, N.N.1    Reguly, T.2    Breitkreutz, A.3    Boucher, L.4    Breitkreutz, B.J.5
  • 13
    • 34147121646 scopus 로고    scopus 로고
    • Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae
    • Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, et al. (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 6(3): 439-450.
    • (2007) Mol Cell Proteomics , vol.6 , Issue.3 , pp. 439-450
    • Collins, S.R.1    Kemmeren, P.2    Zhao, X.C.3    Greenblatt, J.F.4    Spencer, F.5
  • 14
    • 0142052944 scopus 로고    scopus 로고
    • A Bayesian networks approach for predicting protein-protein interactions from genomic data
    • Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, et al. (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302(5644): 449-453.
    • (2003) Science , vol.302 , Issue.5644 , pp. 449-453
    • Jansen, R.1    Yu, H.2    Greenbaum, D.3    Kluger, Y.4    Krogan, N.J.5
  • 15
    • 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 U S A 98(8): 4569-4574.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , Issue.8 , pp. 4569-4574
    • Ito, T.1    Chiba, T.2    Ozawa, R.3    Yoshida, M.4    Hattori, M.5
  • 16
    • 43249125341 scopus 로고    scopus 로고
    • Using protein complexes to predict phenotypic effects of gene mutation
    • Fraser HB, Plotkin JB (2007) Using protein complexes to predict phenotypic effects of gene mutation. Genome Biol 8(11): R252.
    • (2007) Genome Biol , vol.8 , Issue.11
    • Fraser, H.B.1    Plotkin, J.B.2
  • 17
    • 34547787599 scopus 로고    scopus 로고
    • A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality
    • Hart GT, Lee I, Marcotte E (2007) A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics 8(1): 236.
    • (2007) BMC Bioinformatics , vol.8 , Issue.1 , pp. 236
    • Hart, G.T.1    Lee, I.2    Marcotte, E.3
  • 18
    • 0033974688 scopus 로고    scopus 로고
    • Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins
    • Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, et al. (2000) Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci U S A 97(3): 1143-1147.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , Issue.3 , pp. 1143-1147
    • Ito, T.1    Tashiro, K.2    Muta, S.3    Ozawa, R.4    Chiba, T.5
  • 19
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403(6770): 623-627.
    • (2000) Nature , vol.403 , Issue.6770 , pp. 623-627
    • Uetz, P.1    Giot, L.2    Cagney, G.3    Mansfield, T.A.4    Judson, R.S.5
  • 20
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • Gavin AC, 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(6868): 141-147.
    • (2002) Nature , vol.415 , Issue.6868 , pp. 141-147
    • Gavin, A.C.1    Bösche, M.2    Krause, R.3    Grandi, P.4    Marzioch, M.5
  • 21
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
    • Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415(6868): 180-183.
    • (2002) Nature , vol.415 , Issue.6868 , pp. 180-183
    • Ho, Y.1    Gruhler, A.2    Heilbut, A.3    Bader, G.D.4    Moore, L.5
  • 22
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440(7084): 631-636.
    • (2006) Nature , vol.440 , Issue.7084 , pp. 631-636
    • Gavin, A.C.1    Aloy, P.2    Grandi, P.3    Krause, R.4    Boesche, M.5
  • 23
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    • Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440(7084): 637-643.
    • (2006) Nature , vol.440 , Issue.7084 , pp. 637-643
    • Krogan, N.J.1    Cagney, G.2    Yu, H.3    Zhong, G.4    Guo, X.5
  • 24
    • 26244440771 scopus 로고    scopus 로고
    • Gene essentiality and the topology of protein interaction networks
    • Coulomb S, Bauer M, Bernard D, Marsolier-Kergoat MC, et al. (2005) Gene essentiality and the topology of protein interaction networks. Proc Biol Sci 272(1573): 1721-1725.
    • (2005) Proc Biol Sci , vol.272 , Issue.1573 , pp. 1721-1725
    • Coulomb, S.1    Bauer, M.2    Bernard, D.3    Marsolier-Kergoat, M.C.4
  • 25
    • 0037173615 scopus 로고    scopus 로고
    • Functional profiling of the Saccharomyces cerevisiae genome
    • Giaever G, Chu AM, Ni L, Connelly C, Riles L, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418(6896): 387-391.
    • (2002) Nature , vol.418 , Issue.6896 , pp. 387-391
    • Giaever, G.1    Chu, A.M.2    Ni, L.3    Connelly, C.4    Riles, L.5
  • 27
    • 33646563056 scopus 로고    scopus 로고
    • Brandes U, Erlebach T, eds , Berlin, New York: Springer
    • Brandes U, Erlebach T, eds (2005) Network Analysis: Methodological Foundations. Berlin, New York: Springer.
    • (2005) Network Analysis: Methodological Foundations
  • 28
    • 0001316531 scopus 로고
    • Factoring and weighting approaches to status scores and clique identification
    • Bonacich P (1972) Factoring and weighting approaches to status scores and clique identification. J Math Sociol 2(1): 113-120.
    • (1972) J Math Sociol , vol.2 , Issue.1 , pp. 113-120
    • Bonacich, P.1
  • 29
    • 26944450851 scopus 로고    scopus 로고
    • Subgraph centrality in complex networks
    • Estrada E, Rodriguez-Velázquez JA (2005) Subgraph centrality in complex networks. Phys Rev E 71(5): 56103.
    • (2005) Phys Rev E , vol.71 , Issue.5 , pp. 56103
    • Estrada, E.1    Rodriguez-Velázquez, J.A.2
  • 30
    • 84865730611 scopus 로고
    • A set of measures of centrality based on betweenness
    • Freeman LC (1977) A set of measures of centrality based on betweenness. Sociometry 40(1): 35-41.
    • (1977) Sociometry , vol.40 , Issue.1 , pp. 35-41
    • Freeman, L.C.1
  • 31
    • 13944252976 scopus 로고    scopus 로고
    • A measure of betweenness centrality based on random walks
    • Newman MEJ (2005) A measure of betweenness centrality based on random walks. Soc Networks 27: 39-54.
    • (2005) Soc Networks , vol.27 , pp. 39-54
    • Newman, M.E.J.1
  • 33
    • 0031840672 scopus 로고    scopus 로고
    • Molecular genetics of the RNA polymerase II general transcriptional machinery
    • Hampsey M (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol Mol Biol Rev 62(2): 465-503.
    • (1998) Microbiol Mol Biol Rev , vol.62 , Issue.2 , pp. 465-503
    • Hampsey, M.1
  • 34
    • 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 SG, et al. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417(6887): 399-403.
    • (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
  • 35
    • 3042848952 scopus 로고    scopus 로고
    • Evidence for dynamically organized modularity in the yeast protein-protein interaction network
    • Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430(6995): 88-93.
    • (2004) Nature , vol.430 , Issue.6995 , pp. 88-93
    • Han, J.D.1    Bertin, N.2    Hao, T.3    Goldberg, D.S.4    Berriz, G.F.5
  • 36
    • 33845875196 scopus 로고    scopus 로고
    • Relating three-dimensional structures to protein networks provides evolutionary insights
    • Kim PM, Lu LJ, Xia Y, Gerstein MB (2006) Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314(5807): 1938-1941.
    • (2006) Science , vol.314 , Issue.5807 , pp. 1938-1941
    • Kim, P.M.1    Lu, L.J.2    Xia, Y.3    Gerstein, M.B.4
  • 38
    • 20444504323 scopus 로고    scopus 로고
    • Uncovering the overlapping community structure of complex networks in nature and society
    • Palla G, Derényi I, Farkas I, Vicsek T (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435(7043): 814-818.
    • (2005) Nature , vol.435 , Issue.7043 , pp. 814-818
    • Palla, G.1    Derényi, I.2    Farkas, I.3    Vicsek, T.4


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