메뉴 건너뛰기




Volumn 4, Issue , 2014, Pages

Design principles of stripe-forming motifs: The role of positive feedback

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; EMBRYO DEVELOPMENT; FEEDBACK SYSTEM; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; PHYSIOLOGY; RADIATION EXPOSURE;

EID: 84900992907     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep05003     Document Type: Article
Times cited : (17)

References (60)
  • 4
    • 33745780500 scopus 로고    scopus 로고
    • Network motifs: Structure does not determine function
    • Ingram, P. J., Stumpf, M. P. H. & Stark, J. Network motifs: structure does not determine function. BMC Genomics 7, e108 (2006).
    • (2006) BMC Genomics , vol.7
    • Ingram, P.J.1    Stumpf, M.P.H.2    Stark, J.3
  • 5
    • 70350452758 scopus 로고    scopus 로고
    • Understanding modularity in molecular networks requires dynamics
    • Alexander, R. P., Kim, P. M., Emonet, T. & Gerstein, M. B. Understanding modularity in molecular networks requires dynamics. Sci Signal 2, e44 (2009).
    • (2009) Sci Signal , vol.2
    • Alexander, R.P.1    Kim, P.M.2    Emonet, T.3    Gerstein, M.B.4
  • 6
    • 78650362376 scopus 로고    scopus 로고
    • Emerging properties of animal gene regulatory networks
    • Davidson, E. H. Emerging properties of animal gene regulatory networks. Nature 468, 911-920 (2010).
    • (2010) Nature , vol.468 , pp. 911-920
    • Davidson, E.H.1
  • 7
    • 34249079154 scopus 로고    scopus 로고
    • Network motifs: Theory and experimental approaches
    • DOI 10.1038/nrg2102, PII NRG2102
    • Alon, U. Network motifs: theory and experimental approaches. Nat Rev Genet 8, 450-461 (2007). (Pubitemid 46789247)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.6 , pp. 450-461
    • Alon, U.1
  • 8
    • 77951681944 scopus 로고    scopus 로고
    • Functional motifs in biochemical reaction networks
    • Tyson, J. J. &Novák, B. Functional motifs in biochemical reaction networks. Annu Rev Phys Chem 61, 219-240 (2010).
    • (2010) Annu Rev Phys Chem , vol.61 , pp. 219-240
    • Tyson, J.J.1    Novák, B.2
  • 9
    • 80052493200 scopus 로고    scopus 로고
    • Synthetic biology: Integrated gene circuits
    • Nandagopal, N. & Elowitz, M. B. Synthetic biology: integrated gene circuits. Science 333, 1244-1248 (2011).
    • (2011) Science , vol.333 , pp. 1244-1248
    • Nandagopal, N.1    Elowitz, M.B.2
  • 10
    • 70549113260 scopus 로고    scopus 로고
    • Stripe formation in the early fly embryo: Principles, models, and networks
    • Papatsenko, D. Stripe formation in the early fly embryo: principles, models, and networks. Bioessays 31, 1172-1180 (2009).
    • (2009) Bioessays , vol.31 , pp. 1172-1180
    • Papatsenko, D.1
  • 11
    • 0030248501 scopus 로고    scopus 로고
    • One hundred years of positional information
    • Wolpert, L. One hundred years of positional information. Trends Genet 12, 359-364 (1996). (Pubitemid 26294696)
    • (1996) Trends in Genetics , vol.12 , Issue.9 , pp. 359-364
    • Wolpert, L.1
  • 12
    • 33244485265 scopus 로고    scopus 로고
    • The interpretation of morphogen gradients
    • DOI 10.1242/dev.02238
    • Ashe, H. L. & Briscoe, J. The interpretation of morphogen gradients. Development 133, 385-394 (2006). (Pubitemid 43273825)
    • (2006) Development , vol.133 , Issue.3 , pp. 385-394
    • Ashe, H.L.1    Briscoe, J.2
  • 13
    • 4644363054 scopus 로고    scopus 로고
    • Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster
    • DOI 10.1534/genetics.104.027334
    • Jaeger, J. et al. Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster. Genetics 167, 1721-1737 (2004). (Pubitemid 39265909)
    • (2004) Genetics , vol.167 , Issue.4 , pp. 1721-1737
    • Jaeger, J.1
  • 14
    • 77957256791 scopus 로고    scopus 로고
    • Graded dorsal and differential gene regulation in the Drosophila embryo
    • Reeves, G. T. & Stathopoulos, A. Graded dorsal and differential gene regulation in the Drosophila embryo. Cold Spring Harb Perspect Biol 1, e000836 (2009).
    • (2009) Cold Spring Harb Perspect Biol , vol.1
    • Reeves, G.T.1    Stathopoulos, A.2
  • 15
    • 0036894034 scopus 로고    scopus 로고
    • Morphogen gradients, positional information, and Xenopus: Interplay of theory and experiment
    • DOI 10.1002/dvdy.10170
    • Green, J. Morphogen Gradients, Positional Information, and Xenopus: Interplay of Theory and Experiment. Dev Dyn 225, 392-408 (2002). (Pubitemid 35429724)
    • (2002) Developmental Dynamics , vol.225 , Issue.4 , pp. 392-408
    • Green, J.1
  • 16
    • 50649088457 scopus 로고    scopus 로고
    • Pattern formation in the vertebrate neural tube: A sonic hedgehog morphogen-regulated transcriptional network
    • Dessaud, E., McMahon, A. P. & Briscoe, J. Pattern formation in the vertebrate neural tube: a sonic hedgehog morphogen-regulated transcriptional network. Development 135, 2489-2503 (2008).
    • (2008) Development , vol.135 , pp. 2489-2503
    • Dessaud, E.1    McMahon, A.P.2    Briscoe, J.3
  • 17
    • 3142734333 scopus 로고    scopus 로고
    • Dynamic control of positional information in the early Drosophila embryo
    • DOI 10.1038/nature02678
    • Jaeger, J. et al. Dynamic control of positional information in the early Drosophila embryo. Nature 430, 368-371 (2004). (Pubitemid 38937746)
    • (2004) Nature , vol.430 , Issue.6997 , pp. 368-371
    • Jaeger, J.1
  • 18
    • 81955164757 scopus 로고    scopus 로고
    • Spatiotemporal mechanisms ofmorphogen gradient interpretation
    • Nahmad, M. & Lander, A. D. Spatiotemporal mechanisms ofmorphogen gradient interpretation. Curr Opin Genet Dev 21, 726-731 (2011).
    • (2011) Curr Opin Genet Dev , vol.21 , pp. 726-731
    • Nahmad, M.1    Lander, A.D.2
  • 19
    • 84856094426 scopus 로고    scopus 로고
    • Gene regulatory logic for reading the Sonic Hedgehog signaling gradient in the vertebrate neural tube
    • Balaskas, N. et al. Gene regulatory logic for reading the Sonic Hedgehog signaling gradient in the vertebrate neural tube. Cell 148, 273-284 (2012).
    • (2012) Cell , vol.148 , pp. 273-284
    • Balaskas, N.1
  • 20
    • 84867349994 scopus 로고    scopus 로고
    • Predictive computation of genomic logic processing functions in embryonic development
    • Peter, I. S., Faure, E. & Davidson, E. H. Predictive computation of genomic logic processing functions in embryonic development. Proc Natl Acad Sci U S A 111, 906-913 (2012).
    • (2012) Proc Natl Acad Sci U S A , vol.111 , pp. 906-913
    • Peter, I.S.1    Faure, E.2    Davidson, E.H.3
  • 21
    • 84862163583 scopus 로고    scopus 로고
    • Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster
    • Kim, M.-S., Kim, J.-R., Kim, D., Lander, A. D. & Cho, K.-H. Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster. BMC Syst Biol 6, e31 (2012).
    • (2012) BMC Syst Biol , vol.6
    • Kim, M.-S.1    Kim, J.-R.2    Kim, D.3    Lander, A.D.4    Cho, K.-H.5
  • 22
    • 41949100688 scopus 로고    scopus 로고
    • Mutual interaction in network motifs robustly sharpens gene expression in developmental processes
    • Ishihara, S. & Shibata, T. Mutual interaction in network motifs robustly sharpens gene expression in developmental processes. J Theor Biol 252, 131-144 (2008).
    • (2008) J Theor Biol , vol.252 , pp. 131-144
    • Ishihara, S.1    Shibata, T.2
  • 23
    • 47349095809 scopus 로고    scopus 로고
    • The incoherent feed-forward loop can generate non-monotonic input functions for genes
    • Kaplan, S., Bren, A., Dekel, E. & Alon, U. The incoherent feed-forward loop can generate non-monotonic input functions for genes. Mol Syst Biol 4, e203 (2008).
    • (2008) Mol Syst Biol , vol.4
    • Kaplan, S.1    Bren, A.2    Dekel, E.3    Alon, U.4
  • 24
    • 79951939643 scopus 로고    scopus 로고
    • Structural discrimination of robustness in transcriptional feedforward loops for pattern formation
    • Rodrigo, G. & Elena, S. F. Structural Discrimination of Robustness in Transcriptional Feedforward Loops for Pattern Formation. PLoS One 6, e16904 (2011).
    • (2011) PLoS One , vol.6
    • Rodrigo, G.1    Elena, S.F.2
  • 25
    • 17844374314 scopus 로고    scopus 로고
    • A synthetic multicellular system for programmed pattern formation
    • DOI 10.1038/nature03461
    • Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130-1134 (2005). (Pubitemid 40663491)
    • (2005) Nature , vol.434 , Issue.7037 , pp. 1130-1134
    • Basu, S.1    Gerchman, Y.2    Collins, C.H.3    Arnold, F.H.4    Weiss, R.5
  • 26
    • 34249863319 scopus 로고    scopus 로고
    • A mechanism for the sharp transition of morphogen gradient interpretation in Xenopus
    • Saka, Y. & Smith, J. C. A mechanism for the sharp transition of morphogen gradient interpretation in Xenopus. BMC Dev Biol 7, e47 (2007).
    • (2007) BMC Dev Biol , vol.7
    • Saka, Y.1    Smith, J.C.2
  • 27
    • 78649363586 scopus 로고    scopus 로고
    • An engineered mammalian band-pass network
    • Greber, D. & Fussenegger, M. An engineered mammalian band-pass network. Nucleic Acids Res 38, e174 (2010).
    • (2010) Nucleic Acids Res , vol.38
    • Greber, D.1    Fussenegger, M.2
  • 28
    • 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 Syst Biol 6, 425 (2010).
    • (2010) Mol Syst Biol , vol.6 , pp. 425
    • Cotterell, J.1    Sharpe, J.2
  • 31
    • 45549097452 scopus 로고    scopus 로고
    • Positive feedback in cellular control systems
    • DOI 10.1002/bies.20769
    • Mitrophanov, A. Y. & Groisman, E. A. Positive feedback in cellular control systems. Bioessays 30, 542-555 (2008). (Pubitemid 351859411)
    • (2008) BioEssays , vol.30 , Issue.6 , pp. 542-555
    • Mitrophanov, A.Y.1    Groisman, E.A.2
  • 32
    • 67650727380 scopus 로고    scopus 로고
    • Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks
    • Seo, C. H., Kim, J.-R., Kim, M.-S. & Cho, K.-H. Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks. Bioinformatics 25, 1898-1904 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1898-1904
    • Seo, C.H.1    Kim, J.-R.2    Kim, M.-S.3    Cho, K.-H.4
  • 33
    • 0025991216 scopus 로고
    • A connectionist model of development
    • Mjolsness, E., Sharp, D. H. & Reinitz, J. A connectionist model of development. J Theor Biol 152, 429-453 (1991).
    • (1991) J Theor Biol , vol.152 , pp. 429-453
    • Mjolsness, E.1    Sharp, D.H.2    Reinitz, J.3
  • 34
    • 0029107149 scopus 로고
    • Model for cooperative control of positional information in Drosophila by bicoid and maternal hunchback
    • Reinitz, J., Mjolsness, E. &Sharp, D. H. Model for cooperative control of positional information in Drosophila by bicoid and maternal hunchback. J Exp Zool 271, 47-56 (1995).
    • (1995) J Exp Zool , vol.271 , pp. 47-56
    • Reinitz, J.1    Mjolsness, E.2    Sharp, D.H.3
  • 35
    • 0037086147 scopus 로고    scopus 로고
    • Common pattern formation, modularity and phase transitions in a gene network model of morphogenesis
    • DOI 10.1016/S0378-4371(01)00580-5, PII S0378437101005805
    • Solé, R. V., Salazar-Ciudad, I. &Garcia-Fernandez, J. Common pattern formation, modularity and phase transitions in a gene network model of morphogenesis. Physica A 305, 640-654 (2002). (Pubitemid 34232293)
    • (2002) Physica A: Statistical Mechanics and its Applications , vol.305 , Issue.3-4 , pp. 640-654
    • Sole, R.V.1    Salazar-Ciudad, I.2    Garcia-Fernandez, J.3
  • 36
    • 63549100975 scopus 로고    scopus 로고
    • Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors
    • Manu et al. Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors. PLoS Comput Biol 5, e1000303 (2009).
    • (2009) PLoS Comput Biol , vol.5
    • Manu1
  • 37
    • 79151474239 scopus 로고    scopus 로고
    • Understanding gene circuits at cell-fate branch points for rational cell reprogramming
    • Zhou, J. X. & Huang, S. Understanding gene circuits at cell-fate branch points for rational cell reprogramming. Trends Genet 27, 55-62 (2011).
    • (2011) Trends Genet , vol.27 , pp. 55-62
    • Zhou, J.X.1    Huang, S.2
  • 38
    • 27644443808 scopus 로고    scopus 로고
    • Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes
    • DOI 10.1111/j.1365-2443.2005.00897.x
    • Ishihara, S., Fujimoto, K. & Shibata, T. Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes. Genes Cells 10, 1025-1038 (2005). (Pubitemid 41556072)
    • (2005) Genes to Cells , vol.10 , Issue.11 , pp. 1025-1038
    • Ishihara, S.1    Fujimoto, K.2    Shibata, T.3
  • 39
    • 66249088017 scopus 로고    scopus 로고
    • The second wave of synthetic biology: From modules to systems
    • Purnick, P. E. M. & Weiss, R. The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10, 410-422 (2009).
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 410-422
    • Purnick, P.E.M.1    Weiss, R.2
  • 40
    • 37549018487 scopus 로고    scopus 로고
    • Environmental variability and modularity of bacterial metabolic networks
    • Parter, M., Kashtan, N. & Alon, U. Environmental variability and modularity of bacterial metabolic networks. BMC Evol Biol 7, e169 (2007).
    • (2007) BMC Evol Biol , vol.7
    • Parter, M.1    Kashtan, N.2    Alon, U.3
  • 41
    • 84855896286 scopus 로고    scopus 로고
    • Evolvability of feed-forward loop architecture biases its abundance in transcription networks
    • Widder, S., Solé, R. & Macá, J. Evolvability of feed-forward loop architecture biases its abundance in transcription networks. BMC Syst Biol 6, e7 (2012).
    • (2012) BMC Syst Biol , vol.6
    • Widder, S.1    Solé, R.2    Macá, J.3
  • 42
    • 34250684094 scopus 로고    scopus 로고
    • Sharp developmental thresholds defined through bistability by antagonistic gradients of retinoic acid and FGF signaling
    • DOI 10.1002/dvdy.21193
    • Goldbeter, A., Gonze, D. & Pourquié, O. Sharp developmental thresholds defined through bistability by antagonistic gradients of retinoic acid and FGF signaling. Dev Dyn 236, 1495-1508 (2007). (Pubitemid 46932354)
    • (2007) Developmental Dynamics , vol.236 , Issue.6 , pp. 1495-1508
    • Goldbeter, A.1    Gonze, D.2    Pourquie, O.3
  • 43
    • 77954641668 scopus 로고    scopus 로고
    • Modeling bistable cellfate choices in the Drosophila eye: Qualitative and quantitative perspectives
    • Graham, T. G. W., Tabei, S. M. A., Dinner, A. R. &Rebay, I. Modeling bistable cellfate choices in the Drosophila eye: qualitative and quantitative perspectives. Development 137, 2265-2278 (2010).
    • (2010) Development , vol.137 , pp. 2265-2278
    • Graham, T.G.W.1    Tabei, S.M.A.2    Dinner, A.R.3    Rebay, I.4
  • 44
    • 84866107621 scopus 로고    scopus 로고
    • Mutual repression enhances the steepness and precision of gene expression boundaries
    • Sokolowski, T. R., Erdmann, T. & ten Wolde, P. R. Mutual Repression Enhances the Steepness and Precision of Gene Expression Boundaries. PLoS Comput Biol 8, e1002654 (2012).
    • (2012) PLoS Comput Biol , vol.8
    • Sokolowski, T.R.1    Erdmann, T.2    Ten Wolde, P.R.3
  • 45
    • 84866977110 scopus 로고    scopus 로고
    • Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain
    • Zhang, L. et al. Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain. Mol Syst Biol 8, e613 (2012).
    • (2012) Mol Syst Biol , vol.8
    • Zhang, L.1
  • 46
    • 58149145777 scopus 로고    scopus 로고
    • The biphasic behavior of incoherent feedforward loops in biomolecular regulatory networks
    • Kim, D., Kwon, Y.-K. & Cho, K.-H. The biphasic behavior of incoherent feedforward loops in biomolecular regulatory networks. Bioessays 30, 1204-1211 (2008).
    • (2008) Bioessays , vol.30 , pp. 1204-1211
    • Kim, D.1    Kwon, Y.-K.2    Cho, K.-H.3
  • 47
    • 71049182983 scopus 로고    scopus 로고
    • Specialized or flexible feed-forward loop motifs: A question of topology
    • Macá, J., Widder, S. & Solé, R. Specialized or flexible feed-forward loop motifs: a question of topology. BMC Syst Biol 3, e84 (2009).
    • (2009) BMC Syst Biol , vol.3
    • Macá, J.1    Widder, S.2    Solé, R.3
  • 48
    • 71149099313 scopus 로고    scopus 로고
    • The incoherent feedforward loop can provide fold-change detection in gene regulation
    • Goentoro, L., Shoval, O., Kirschner, M. W. &Alon, U. The incoherent feedforward loop can provide fold-change detection in gene regulation. Mol Cell 36, 894-899 (2009).
    • (2009) Mol Cell , vol.36 , pp. 894-899
    • Goentoro, L.1    Shoval, O.2    Kirschner, M.W.3    Alon, U.4
  • 49
    • 77950960454 scopus 로고    scopus 로고
    • Optimizing information flow in small genetic networks. II. Feed-forward interactions
    • Walczak, A. M., Tkacik, G. & Bialek, W. Optimizing information flow in small genetic networks. II. Feed-forward interactions. Phys Rev E Stat Nonlin Soft Matter Phys 81, 041905 (2010).
    • (2010) Phys Rev e Stat Nonlin Soft Matter Phys , vol.81 , pp. 041905
    • Walczak, A.M.1    Tkacik, G.2    Bialek, W.3
  • 50
    • 79952302623 scopus 로고    scopus 로고
    • The role of incoherent microRNAmediated feedforward loops in noise buffering
    • Osella, M., Bosia, C., Corá, D. & Caselle, M. The role of incoherent microRNAmediated feedforward loops in noise buffering. PLoS Comput Biol 7, e1001101 (2011).
    • (2011) PLoS Comput Biol , vol.7
    • Osella, M.1    Bosia, C.2    Corá, D.3    Caselle, M.4
  • 52
    • 34249722123 scopus 로고    scopus 로고
    • Enhancer responses to similarly distributed antagonistic gradients in development
    • Zinzen, R. P. & Papatsenko, D. Enhancer responses to similarly distributed antagonistic gradients in development. PLoS Comput Biol 3, e84 (2007).
    • (2007) PLoS Comput Biol , vol.3
    • Zinzen, R.P.1    Papatsenko, D.2
  • 53
    • 36849086569 scopus 로고    scopus 로고
    • Enhancer organization: Transistor with a twist or something in a different vein
    • Zartman, J. J. &Shvartsman, S. Y. Enhancer organization: transistor with a twist or something in a different vein Curr Biol 17, 1048-1050 (2007).
    • (2007) Curr Biol , vol.17 , pp. 1048-1050
    • Zartman, J.J.1    Shvartsman, S.Y.2
  • 54
    • 62549105372 scopus 로고    scopus 로고
    • Pattern formation by dynamically interacting network motifs
    • Lembong, J., Yakoby, N. & Shvartsman, S. Y. Pattern formation by dynamically interacting network motifs. Proc Natl Acad Sci U S A 106, 3213-3218 (2009).
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 3213-3218
    • Lembong, J.1    Yakoby, N.2    Shvartsman, S.Y.3
  • 55
    • 79952633685 scopus 로고    scopus 로고
    • Pattern, growth, and control
    • Lander, A. D. Pattern, growth, and control. Cell 144, 955-969 (2011).
    • (2011) Cell , vol.144 , pp. 955-969
    • Lander, A.D.1
  • 56
    • 80054020133 scopus 로고    scopus 로고
    • Morphogen gradients: From generation to interpretation
    • Rogers, K. W. & Schier, A. F. Morphogen gradients: from generation to interpretation. Annu Rev Cell Dev Biol 27, 377-407 (2011).
    • (2011) Annu Rev Cell Dev Biol , vol.27 , pp. 377-407
    • Rogers, K.W.1    Schier, A.F.2
  • 58
    • 77952701988 scopus 로고    scopus 로고
    • Dynamic network rewiring determines temporal regulatory functions in Drosophila melanogaster development processes
    • Kim, M.-S., Kim, J.-R. & Cho, K.-H. Dynamic network rewiring determines temporal regulatory functions in Drosophila melanogaster development processes. BioEssays 32, 505-513 (2010).
    • (2010) BioEssays , vol.32 , pp. 505-513
    • Kim, M.-S.1    Kim, J.-R.2    Cho, K.-H.3
  • 59
    • 70350336588 scopus 로고    scopus 로고
    • Architecture-dependent noise discriminates functionally analogous differentiation circuits
    • Cagatay, T., Turcotte, M., Elowitz, M. B., Garcia-Ojalvo, J. & Süel, G. M. Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139, 512-522 (2009).
    • (2009) Cell , vol.139 , pp. 512-522
    • Cagatay, T.1    Turcotte, M.2    Elowitz, M.B.3    Garcia-Ojalvo, J.4    Süel, G.M.5
  • 60
    • 35348827221 scopus 로고    scopus 로고
    • Evolution of robustness to noise and mutation in gene expression dynamics
    • Kaneko, K. Evolution of robustness to noise and mutation in gene expression dynamics. PLoS One 2, e434 (2007).
    • (2007) PLoS One , vol.2
    • Kaneko, K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.