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Volumn 3, Issue 10, 2007, Pages 1993-2002

Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network

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EID: 35748958993     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030198     Document Type: Article
Times cited : (38)

References (50)
  • 1
    • 14644396645 scopus 로고    scopus 로고
    • Functional cartography of complex metabolic networks
    • Guimera R, Nunes Amaral LA (2005) Functional cartography of complex metabolic networks. Nature 433: 895-900.
    • (2005) Nature , vol.433 , pp. 895-900
    • Guimera, R.1    Nunes Amaral, L.A.2
  • 2
    • 0034943378 scopus 로고    scopus 로고
    • The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes
    • Wagner A (2001) The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol 18: 1283-1292.
    • (2001) Mol Biol Evol , vol.18 , pp. 1283-1292
    • Wagner, A.1
  • 3
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31: 64-68.
    • (2002) Nat Genet , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 4
    • 0034029892 scopus 로고    scopus 로고
    • Robustness against mutations in genetic networks of yeast
    • Wagner A (2000) Robustness against mutations in genetic networks of yeast. Nat Genet 24: 355-361.
    • (2000) Nat Genet , vol.24 , pp. 355-361
    • Wagner, A.1
  • 5
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: A brief overview
    • Kitano H (2002) Systems biology: A brief overview. Science 295: 1662-1664.
    • (2002) Science , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 7
    • 25444448797 scopus 로고    scopus 로고
    • Spontaneous evolution of modularity and network motifs
    • Kashtan N, Alon U (2005) Spontaneous evolution of modularity and network motifs. Proc Natl Acad Sci U S A 102: 13773-13778.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 13773-13778
    • Kashtan, N.1    Alon, U.2
  • 8
    • 1942469444 scopus 로고    scopus 로고
    • Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction
    • Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, et al. (2004) Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci U S A 101: 5934-5939.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 5934-5939
    • Yeger-Lotem, E.1    Sattath, S.2    Kashtan, N.3    Itzkovitz, S.4    Milo, R.5
  • 9
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342.
    • (2000) Nature , vol.403 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 11
    • 2442537233 scopus 로고    scopus 로고
    • Gene regulatory network growth by duplication
    • Teichmann SA, Babu MM (2004) Gene regulatory network growth by duplication. Nat Genet 36: 492-496.
    • (2004) Nat Genet , vol.36 , pp. 492-496
    • Teichmann, S.A.1    Babu, M.M.2
  • 12
    • 3042722019 scopus 로고    scopus 로고
    • Evolutionary changes in cis and trans gene regulation
    • Wittkopp PJ, Haerum BK, Clark AG (2004) Evolutionary changes in cis and trans gene regulation. Nature 430: 85-88.
    • (2004) Nature , vol.430 , pp. 85-88
    • Wittkopp, P.J.1    Haerum, B.K.2    Clark, A.G.3
  • 13
    • 48949094754 scopus 로고    scopus 로고
    • Local regulatory variation in Saccharomyces cerevisiae
    • doi:10.1371/journal.pgen.0010025
    • Ronald J, Brem RB, Whittle J, Kruglyak L (2005) Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet 1: e25. doi:10.1371/journal.pgen.0010025
    • (2005) PLoS Genet , vol.1
    • Ronald, J.1    Brem, R.B.2    Whittle, J.3    Kruglyak, L.4
  • 14
    • 0030947344 scopus 로고    scopus 로고
    • Molecular evidence for an ancient duplication of the entire yeast genome
    • Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
    • (1997) Nature , vol.387 , pp. 708-713
    • Wolfe, K.H.1    Shields, D.C.2
  • 15
    • 1942452749 scopus 로고    scopus 로고
    • Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
    • Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
    • (2004) Nature , vol.428 , pp. 617-624
    • Kellis, M.1    Birren, B.W.2    Lander, E.S.3
  • 16
    • 2942552376 scopus 로고    scopus 로고
    • Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network
    • Dobrin R, Beg QK, Barabasi AL, Oltvai ZN (2004) Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. BMC Bioinformatics 5: 10.
    • (2004) BMC Bioinformatics , vol.5 , pp. 10
    • Dobrin, R.1    Beg, Q.K.2    Barabasi, A.L.3    Oltvai, Z.N.4
  • 17
    • 8844244033 scopus 로고    scopus 로고
    • Very low gene duplication rate in the yeast genome
    • Gao LZ, Innan H (2004) Very low gene duplication rate in the yeast genome. Science 306: 1367-1370.
    • (2004) Science , vol.306 , pp. 1367-1370
    • Gao, L.Z.1    Innan, H.2
  • 18
    • 0036613237 scopus 로고    scopus 로고
    • Extensive genomic duplication during early chordate evolution
    • McLysaght A, Hokamp K, Wolfe KH (2002) Extensive genomic duplication during early chordate evolution. Nat Genet 31: 200-204.
    • (2002) Nat Genet , vol.31 , pp. 200-204
    • McLysaght, A.1    Hokamp, K.2    Wolfe, K.H.3
  • 19
    • 0035081235 scopus 로고    scopus 로고
    • Gene duplication and the structure of eukaryotic genomes
    • Friedman R, Hughes AL (2001) Gene duplication and the structure of eukaryotic genomes. Genome Res 11: 373-381.
    • (2001) Genome Res , vol.11 , pp. 373-381
    • Friedman, R.1    Hughes, A.L.2
  • 21
    • 0036578654 scopus 로고    scopus 로고
    • Topological and causal structure of the yeast transcriptional regulatory network
    • Guelzim N, Bottani S, Bourgine P, Kepes F (2002) Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 31: 60-63.
    • (2002) Nat Genet , vol.31 , pp. 60-63
    • Guelzim, N.1    Bottani, S.2    Bourgine, P.3    Kepes, F.4
  • 22
    • 9244257298 scopus 로고    scopus 로고
    • Interacting models of cooperative gene regulation
    • Das D, Banerjee N, Zhang M (2004) Interacting models of cooperative gene regulation. Proc Natl Acad Sci U S A 101: 16234-16239.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 16234-16239
    • Das, D.1    Banerjee, N.2    Zhang, M.3
  • 23
    • 0032499071 scopus 로고    scopus 로고
    • Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein-protein interactions
    • Vashee S, Melcher K, Ding WV, Johnston SA, Kodadek T (1998) Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein-protein interactions. Curr Biol 8: 452-458.
    • (1998) Curr Biol , vol.8 , pp. 452-458
    • Vashee, S.1    Melcher, K.2    Ding, W.V.3    Johnston, S.A.4    Kodadek, T.5
  • 25
    • 0029879360 scopus 로고    scopus 로고
    • The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE)
    • Martinez-Pastor MT, Marchler G, Schuller C, Marchler-Bauer A, Ruis H, et al. (1996) The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE). EMBO J 15: 2227-2235.
    • (1996) EMBO J , vol.15 , pp. 2227-2235
    • Martinez-Pastor, M.T.1    Marchler, G.2    Schuller, C.3    Marchler-Bauer, A.4    Ruis, H.5
  • 26
    • 33646167129 scopus 로고    scopus 로고
    • Plasticity of the cis-regulatory input function of a gene
    • doi:10.1371/journal.pbio.0040045
    • Mayo AE, Setty Y, Shavit S, Zaslaver A, Alon U (2006) Plasticity of the cis-regulatory input function of a gene. PLoS Biol 4: e45. doi:10.1371/journal.pbio.0040045
    • (2006) PLoS Biol , vol.4
    • Mayo, A.E.1    Setty, Y.2    Shavit, S.3    Zaslaver, A.4    Alon, U.5
  • 27
    • 0035883741 scopus 로고    scopus 로고
    • Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: Implications for regulating the cell cycle and differentiation
    • Hollenhorst PC, Pietz G, Fox CA (2001) Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: Implications for regulating the cell cycle and differentiation. Genes Dev 15: 2445-2456.
    • (2001) Genes Dev , vol.15 , pp. 2445-2456
    • Hollenhorst, P.C.1    Pietz, G.2    Fox, C.A.3
  • 28
    • 0033972072 scopus 로고    scopus 로고
    • The probability of duplicate gene preservation by subfunctionalization
    • Lynch M, Force A (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459-473.
    • (2000) Genetics , vol.154 , pp. 459-473
    • Lynch, M.1    Force, A.2
  • 29
    • 0035697435 scopus 로고    scopus 로고
    • The probability of preservation of a newly arisen gene duplicate
    • Lynch M, O'Hely M, Walsh B, Force A (2001) The probability of preservation of a newly arisen gene duplicate. Genetics 159: 1789-1804.
    • (2001) Genetics , vol.159 , pp. 1789-1804
    • Lynch, M.1    O'Hely, M.2    Walsh, B.3    Force, A.4
  • 30
    • 0036792156 scopus 로고    scopus 로고
    • Asymmetric functional divergence of duplicate genes in yeast
    • Wagner A (2002) Asymmetric functional divergence of duplicate genes in yeast. Mol Biol Evol 19: 1760-1768.
    • (2002) Mol Biol Evol , vol.19 , pp. 1760-1768
    • Wagner, A.1
  • 32
    • 0142027814 scopus 로고    scopus 로고
    • Structure and function of the feed-forward loop network motif
    • Mangan S, Alon U (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 100: 11980-11985.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 11980-11985
    • Mangan, S.1    Alon, U.2
  • 34
    • 33745012299 scopus 로고    scopus 로고
    • Modularity and community structure in networks
    • Newman MEJ (2006) Modularity and community structure in networks. Proc Natl Acad Sci U S A 103: 8577-8582.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 8577-8582
    • Newman, M.E.J.1
  • 35
    • 33746207758 scopus 로고    scopus 로고
    • Bacterial regulatory networks are extremely flexible in evolution
    • Lozada-Chavez I, Janga SC, Collado-Vides J (2006) Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res 34: 3434-3445.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3434-3445
    • Lozada-Chavez, I.1    Janga, S.C.2    Collado-Vides, J.3
  • 36
    • 0038157152 scopus 로고    scopus 로고
    • Dosage sensitivity and the evolution of gene families in yeast
    • Papp B, Pal C, Hurst LD (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194-197.
    • (2003) Nature , vol.424 , pp. 194-197
    • Papp, B.1    Pal, C.2    Hurst, L.D.3
  • 37
  • 38
    • 19544389317 scopus 로고    scopus 로고
    • Energy constraints on the evolution of gene expression
    • Wagner A (2005) Energy constraints on the evolution of gene expression. Mol Biol Evol 22: 1365-1374.
    • (2005) Mol Biol Evol , vol.22 , pp. 1365-1374
    • Wagner, A.1
  • 39
    • 0041704531 scopus 로고    scopus 로고
    • Evolution of cis-regulatory elements in duplicated genes of yeast
    • Papp B, Pal C, Hurst LD (2003) Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet 19: 417-422.
    • (2003) Trends Genet , vol.19 , pp. 417-422
    • Papp, B.1    Pal, C.2    Hurst, L.D.3
  • 40
    • 2942615357 scopus 로고    scopus 로고
    • Upstream plasticity and downstream robustness in evolution of molecular networks
    • Maslov S, Sneppen K, Eriksen KA, Yan KK (2004) Upstream plasticity and downstream robustness in evolution of molecular networks. BMC Evol Biol 4: 9.
    • (2004) BMC Evol Biol , vol.4 , pp. 9
    • Maslov, S.1    Sneppen, K.2    Eriksen, K.A.3    Yan, K.K.4
  • 41
    • 28844434073 scopus 로고    scopus 로고
    • An evolutionary and functional assessment of regulatory network motifs
    • Mazurie A, Bottani S, Vergassola M (2005) An evolutionary and functional assessment of regulatory network motifs. Genome Biol 6: R35.
    • (2005) Genome Biol , vol.6
    • Mazurie, A.1    Bottani, S.2    Vergassola, M.3
  • 42
    • 25144525014 scopus 로고    scopus 로고
    • Core transcriptional regulatory circuitry in human embryonic stem cells
    • Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, et al. (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122: 947-956.
    • (2005) Cell , vol.122 , pp. 947-956
    • Boyer, L.A.1    Lee, T.I.2    Cole, M.F.3    Johnstone, S.E.4    Levine, S.S.5
  • 43
    • 25844471721 scopus 로고    scopus 로고
    • The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species
    • Byrne KP, Wolfe KH (2005) The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 15: 1456-1461.
    • (2005) Genome Res , vol.15 , pp. 1456-1461
    • Byrne, K.P.1    Wolfe, K.H.2
  • 44
    • 0036074510 scopus 로고    scopus 로고
    • Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity
    • Luscombe NM, Thornton JM (2002) Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity. J Mol Biol 320: 991-1009.
    • (2002) J Mol Biol , vol.320 , pp. 991-1009
    • Luscombe, N.M.1    Thornton, J.M.2
  • 45
    • 1842505125 scopus 로고    scopus 로고
    • Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics
    • Sandelin A, Wasserman WW (2004) Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J Mol Biol 338: 207-215.
    • (2004) J Mol Biol , vol.338 , pp. 207-215
    • Sandelin, A.1    Wasserman, W.W.2
  • 46
    • 0037743679 scopus 로고    scopus 로고
    • Convergent evolution of gene circuits
    • Conant GC, Wagner A (2003) Convergent evolution of gene circuits. Nat Genet 34: 264-266.
    • (2003) Nat Genet , vol.34 , pp. 264-266
    • Conant, G.C.1    Wagner, A.2
  • 48
    • 0030712874 scopus 로고    scopus 로고
    • Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions
    • Fernandes L, Rodrigues-Pousada C, Struhl K (1997) Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions. Mol Cell Biol 17: 6982-6993.
    • (1997) Mol Cell Biol , vol.17 , pp. 6982-6993
    • Fernandes, L.1    Rodrigues-Pousada, C.2    Struhl, K.3
  • 49
    • 0027994717 scopus 로고
    • Toward a code for the interactions of zinc fingers with DNA: Selection of randomized fingers displayed on phage
    • Choo Y, Klug A (1994) Toward a code for the interactions of zinc fingers with DNA: Selection of randomized fingers displayed on phage. Proc Natl Acad Sci U S A 91: 11163-11167.
    • (1994) Proc Natl Acad Sci U S A , vol.91 , pp. 11163-11167
    • Choo, Y.1    Klug, A.2
  • 50
    • 0027331505 scopus 로고
    • How do "Zn2 cys6" proteins distinguish between similar upstream activation sites? Comparison of the DNA-binding specificity of the GAL4 protein in vitro and in vivo
    • Vashee S, Xu H, Johnston SA, Kodadek T (1993) How do "Zn2 cys6" proteins distinguish between similar upstream activation sites? Comparison of the DNA-binding specificity of the GAL4 protein in vitro and in vivo. J Biol Chem 268: 24699-24706.
    • (1993) J Biol Chem , vol.268 , pp. 24699-24706
    • Vashee, S.1    Xu, H.2    Johnston, S.A.3    Kodadek, T.4


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