메뉴 건너뛰기




Volumn 6, Issue , 2012, Pages

Evolvability of feed-forward loop architecture biases its abundance in transcription networks

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; FEEDBACK SYSTEM; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; PHYSIOLOGY; STATISTICAL DISTRIBUTION; SYSTEMS BIOLOGY;

EID: 84855896286     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-7     Document Type: Article
Times cited : (13)

References (32)
  • 1
    • 0032555135 scopus 로고    scopus 로고
    • Evolvability
    • 10.1073/pnas.95.15.8420, 33871, 9671692
    • Kirschner M, Gerhart J. Evolvability. Proc Natl Acad Sci USA 1998, 95:8420-7. 10.1073/pnas.95.15.8420, 33871, 9671692.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 8420-8427
    • Kirschner, M.1    Gerhart, J.2
  • 2
    • 36348992094 scopus 로고    scopus 로고
    • Robustness and evolvability: a paradox resolved
    • Wagner A. Robustness and evolvability: a paradox resolved. Proc R Soc London B 2008, 275:91-100.
    • (2008) Proc R Soc London B , vol.275 , pp. 91-100
    • Wagner, A.1
  • 3
    • 0034667684 scopus 로고    scopus 로고
    • Plasticity, evolvability, and modularity in RNA
    • 10.1002/1097-010X(20001015)288:3<242::AID-JEZ5>3.0.CO;2-O, 11069142
    • Ancel LW, Fontana W. Plasticity, evolvability, and modularity in RNA. J Exp Zool 2000, 288:242-83. 10.1002/1097-010X(20001015)288:3<242::AID-JEZ5>3.0.CO;2-O, 11069142.
    • (2000) J Exp Zool , vol.288 , pp. 242-283
    • Ancel, L.W.1    Fontana, W.2
  • 4
    • 0035930008 scopus 로고    scopus 로고
    • The topology of the possible: formal spaces underlying patterns of evolutionary change
    • 10.1006/jtbi.2001.2423, 11894994
    • Stadler B, Stadler P, Wagner G, Fontana W. The topology of the possible: formal spaces underlying patterns of evolutionary change. J theor Biol 2001, 213:241-274. 10.1006/jtbi.2001.2423, 11894994.
    • (2001) J theor Biol , vol.213 , pp. 241-274
    • Stadler, B.1    Stadler, P.2    Wagner, G.3    Fontana, W.4
  • 5
    • 34249079154 scopus 로고    scopus 로고
    • Network motifs: theory and experimental approaches
    • 10.1038/nrg2102, 17510665
    • Alon U. Network motifs: theory and experimental approaches. Nature Reviews Genetics 2007, 8:450-61. 10.1038/nrg2102, 17510665.
    • (2007) Nature Reviews Genetics , vol.8 , pp. 450-461
    • Alon, U.1
  • 6
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: simple building blocks of complex networks
    • 10.1126/science.298.5594.824, 12399590
    • Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: simple building blocks of complex networks. Science 2002, 298:824-7. 10.1126/science.298.5594.824, 12399590.
    • (2002) Science , vol.298 , pp. 824-827
    • Milo, R.1    Shen-Orr, S.2    Itzkovitz, S.3    Kashtan, N.4    Chklovskii, D.5    Alon, U.6
  • 7
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • 10.1038/ng881, 11967538
    • Shen-Orr SS, Milo R, Mangan S, Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 2002, 31:64-8. 10.1038/ng881, 11967538.
    • (2002) Nat Genet , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 8
    • 0242364231 scopus 로고    scopus 로고
    • The Coherent Feedforward Loop Serves as a Sign-sensitive Delay Element in Transcription Networks
    • 10.1016/j.jmb.2003.09.049, 14607112
    • Mangan S, Zaslaver A, Alon U. The Coherent Feedforward Loop Serves as a Sign-sensitive Delay Element in Transcription Networks. J Mol Biol 2003, 334:197-204. 10.1016/j.jmb.2003.09.049, 14607112.
    • (2003) J Mol Biol , vol.334 , pp. 197-204
    • Mangan, S.1    Zaslaver, A.2    Alon, U.3
  • 9
    • 19444376022 scopus 로고    scopus 로고
    • Multiple Functions of a Feed-Forward-Loop Gene Circuit
    • Wall M, Dunlop MJ, Hlavacek W. Multiple Functions of a Feed-Forward-Loop Gene Circuit. JMB 2005, 349:501-14.
    • (2005) JMB , vol.349 , pp. 501-514
    • Wall, M.1    Dunlop, M.J.2    Hlavacek, W.3
  • 10
    • 1442354192 scopus 로고    scopus 로고
    • Multistability in the lactose utilization network of Escherichia coli
    • 10.1038/nature02298, 14973486
    • Ozbudak EM, Thattai M, Lim HN, Shraiman BI, Oudenaarden AV. Multistability in the lactose utilization network of Escherichia coli. Nature 2004, 427:737-40. 10.1038/nature02298, 14973486.
    • (2004) Nature , vol.427 , pp. 737-740
    • Ozbudak, E.M.1    Thattai, M.2    Lim, H.N.3    Shraiman, B.I.4    Oudenaarden, A.V.5
  • 11
    • 0033552946 scopus 로고    scopus 로고
    • Robustness in bacterial chemotaxis
    • 10.1038/16483, 9923680
    • Alon U, Surette MG, Barkai N, Leibler S. Robustness in bacterial chemotaxis. Nature 1999, 397:168-71. 10.1038/16483, 9923680.
    • (1999) Nature , vol.397 , pp. 168-171
    • Alon, U.1    Surette, M.G.2    Barkai, N.3    Leibler, S.4
  • 12
    • 0030797355 scopus 로고    scopus 로고
    • Robustness in simple biochemical networks
    • 10.1038/43072, 9202115
    • Barkai N, Leibler S. Robustness in simple biochemical networks. Nature 1997, 387:855-7. 10.1038/43072, 9202115.
    • (1997) Nature , vol.387 , pp. 855-857
    • Barkai, N.1    Leibler, S.2
  • 13
    • 27644443808 scopus 로고    scopus 로고
    • Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes
    • 10.1111/j.1365-2443.2005.00897.x, 16236132
    • Ishihara S, Fujimoto K, Shibata T. Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes. Genes Cells 2005, 10:1025-1038. 10.1111/j.1365-2443.2005.00897.x, 16236132.
    • (2005) Genes Cells , vol.10 , pp. 1025-1038
    • Ishihara, S.1    Fujimoto, K.2    Shibata, T.3
  • 14
    • 78049513394 scopus 로고    scopus 로고
    • An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients
    • Cotterell J, Sharpe J. An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients. Mol Sys Biol 2010, 6:425-438.
    • (2010) Mol Sys Biol , vol.6 , pp. 425-438
    • Cotterell, J.1    Sharpe, J.2
  • 15
    • 0142027814 scopus 로고    scopus 로고
    • Structure and function of the feed-forward loop network motif
    • 10.1073/pnas.2133841100, 218699, 14530388
    • Mangan S, Alon U. Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA 2003, 100:11980-5. 10.1073/pnas.2133841100, 218699, 14530388.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 11980-11985
    • Mangan, S.1    Alon, U.2
  • 16
    • 33746428728 scopus 로고    scopus 로고
    • A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli
    • 2005.0006
    • Kalir S, Mangan S. A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol Syst Biol 2005, 1. 2005.0006.
    • (2005) Mol Syst Biol , vol.1
    • Kalir, S.1    Mangan, S.2
  • 17
    • 39749111957 scopus 로고    scopus 로고
    • Evolution of evolvability in a developmental model
    • 10.1111/j.1558-5646.2007.00303.x, 18031304
    • Draghi J, Wagner GP. Evolution of evolvability in a developmental model. Evolution 2008, 62:301-15. 10.1111/j.1558-5646.2007.00303.x, 18031304.
    • (2008) Evolution , vol.62 , pp. 301-315
    • Draghi, J.1    Wagner, G.P.2
  • 18
    • 27844551326 scopus 로고    scopus 로고
    • Dynamic properties of network motifs contribute to biological network organization
    • 10.1371/journal.pbio.0030343, 1239925, 16187794
    • Prill RJ, Iglesias PA, Levchenko A. Dynamic properties of network motifs contribute to biological network organization. PLoS Biol 2005, 3:e343. 10.1371/journal.pbio.0030343, 1239925, 16187794.
    • (2005) PLoS Biol , vol.3
    • Prill, R.J.1    Iglesias, P.A.2    Levchenko, A.3
  • 19
    • 24144451839 scopus 로고    scopus 로고
    • Noise characteristics of feed forward loops
    • 10.1088/1478-3967/2/1/005, 16204855
    • Ghosh B, Karmakar R, Bose I. Noise characteristics of feed forward loops. Phys Biol 2005, 2:36-45. 10.1088/1478-3967/2/1/005, 16204855.
    • (2005) Phys Biol , vol.2 , pp. 36-45
    • Ghosh, B.1    Karmakar, R.2    Bose, I.3
  • 20
    • 33748773071 scopus 로고    scopus 로고
    • Feed-forward loop circuits as a side effect of genome evolution
    • 10.1093/molbev/msl060, 16840361
    • Cordero OX, Hogeweg P. Feed-forward loop circuits as a side effect of genome evolution. Mol Biol Evol 2006, 23:1931-6. 10.1093/molbev/msl060, 16840361.
    • (2006) Mol Biol Evol , vol.23 , pp. 1931-1936
    • Cordero, O.X.1    Hogeweg, P.2
  • 21
    • 33745780500 scopus 로고    scopus 로고
    • Network motifs: structure does not determine function
    • 10.1186/1471-2164-7-108, 1488845, 16677373
    • Ingram PJ, Stumpf MP, Stark J. Network motifs: structure does not determine function. BMC Genomics 2006, 7:108. 10.1186/1471-2164-7-108, 1488845, 16677373.
    • (2006) BMC Genomics , vol.7 , pp. 108
    • Ingram, P.J.1    Stumpf, M.P.2    Stark, J.3
  • 22
    • 34548724489 scopus 로고    scopus 로고
    • The evolution of genetic networks by nonadaptive processes
    • Lynch M. The evolution of genetic networks by nonadaptive processes. Nat Rev Genet 2007, 8:803-813.
    • (2007) Nat Rev Genet , vol.8 , pp. 803-813
    • Lynch, M.1
  • 23
    • 33745998748 scopus 로고    scopus 로고
    • Are network motifs the spandrels of cellular complexity?
    • 10.1016/j.tree.2006.05.013, 16764967
    • Solé RV, Valverde S. Are network motifs the spandrels of cellular complexity?. Trends Ecol Evol 2006, 21:419-22. 10.1016/j.tree.2006.05.013, 16764967.
    • (2006) Trends Ecol Evol , vol.21 , pp. 419-422
    • Solé, R.V.1    Valverde, S.2
  • 24
    • 36348960081 scopus 로고    scopus 로고
    • Spontaneous emergence of modularity in cellular networks
    • 10.1098/rsif.2007.1108, 2605507, 17626003
    • Solé RV, Valverde S. Spontaneous emergence of modularity in cellular networks. J R Soc Interface 2008, 5:129-33. 10.1098/rsif.2007.1108, 2605507, 17626003.
    • (2008) J R Soc Interface , vol.5 , pp. 129-133
    • Solé, R.V.1    Valverde, S.2
  • 25
    • 28844434073 scopus 로고    scopus 로고
    • An evolutionary and functional assessment of regulatory network motifs
    • 10.1186/gb-2005-6-4-r35, 1088963, 15833122
    • Mazurie A, Bottani S, Vergassola M. An evolutionary and functional assessment of regulatory network motifs. Genome Biol 2005, 6:R35. 10.1186/gb-2005-6-4-r35, 1088963, 15833122.
    • (2005) Genome Biol , vol.6
    • Mazurie, A.1    Bottani, S.2    Vergassola, M.3
  • 26
    • 71049182983 scopus 로고    scopus 로고
    • Specialized or flexible feed-forward loop motifs: a question of topology
    • Macía J, Widder S, Solé RV. Specialized or flexible feed-forward loop motifs: a question of topology. BMC Syst Biol 2009, 31:3-84.
    • (2009) BMC Syst Biol , vol.31 , pp. 3-84
    • Macía, J.1    Widder, S.2    Solé, R.V.3
  • 27
    • 32044462728 scopus 로고    scopus 로고
    • The Incoherent Feed-forward Loop Accelerates the Response-time of the gal System of Escherichia coli
    • 10.1016/j.jmb.2005.12.003, 16406067
    • Mangan S, Itzkovitz S, Zaslaver A, Alon U. The Incoherent Feed-forward Loop Accelerates the Response-time of the gal System of Escherichia coli. J Mol Biol 2006, 356:1073-81. 10.1016/j.jmb.2005.12.003, 16406067.
    • (2006) J Mol Biol , vol.356 , pp. 1073-1081
    • Mangan, S.1    Itzkovitz, S.2    Zaslaver, A.3    Alon, U.4
  • 28
    • 0037743679 scopus 로고    scopus 로고
    • Convergent evolution of gene circuits
    • 10.1038/ng1181, 12819781
    • Conant GC, Wagner A. Convergent evolution of gene circuits. Nat Genet 2003, 34:264-266. 10.1038/ng1181, 12819781.
    • (2003) Nat Genet , vol.34 , pp. 264-266
    • Conant, G.C.1    Wagner, A.2
  • 29
    • 2442537233 scopus 로고    scopus 로고
    • Gene regulatory network growth by duplication
    • 10.1038/ng1340, 15107850
    • Teichmann SA, Babu MM. Gene regulatory network growth by duplication. Nat Genet 2004, 36:492-496. 10.1038/ng1340, 15107850.
    • (2004) Nat Genet , vol.36 , pp. 492-496
    • Teichmann, S.A.1    Babu, M.M.2
  • 31
    • 0007383359 scopus 로고
    • Calculus
    • Cambridge University Press
    • Spivak M. Calculus. 1994, 201-11. Cambridge University Press.
    • (1994) , pp. 201-211
    • Spivak, M.1
  • 32
    • 84856043672 scopus 로고
    • A Mathematical Theory of Communication
    • Shannon CE. A Mathematical Theory of Communication. Bell System Technical Journal 1948, 27:379-423.
    • (1948) Bell System Technical Journal , vol.27 , pp. 379-423
    • Shannon, C.E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.