메뉴 건너뛰기




Volumn 251, Issue 2, 2008, Pages 363-379

Mathematical classification of regulatory logics for compound environmental changes

Author keywords

Compound control; Control logics; Equivalence class; Gene regulatory unit; Logical functions

Indexed keywords

LACTOSE;

EID: 39649093884     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2007.11.023     Document Type: Article
Times cited : (14)

References (42)
  • 1
    • 0036901602 scopus 로고    scopus 로고
    • Modeling transcriptional regulatory networks
    • Bolouri H., and Davidson E.H. Modeling transcriptional regulatory networks. BioEssays 24 (2002) 1118-1129
    • (2002) BioEssays , vol.24 , pp. 1118-1129
    • Bolouri, H.1    Davidson, E.H.2
  • 2
    • 1842591130 scopus 로고    scopus 로고
    • The regulation of bacterial transcription initiation
    • Browning D.F., and Busby S.J.W. The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2 (2004) 57-65
    • (2004) Nat. Rev. Microbiol. , vol.2 , pp. 57-65
    • Browning, D.F.1    Busby, S.J.W.2
  • 3
    • 0037965981 scopus 로고    scopus 로고
    • On schemes of combinatorial transcription logic
    • Buchler N.E., Gerland U., and Hwa T. On schemes of combinatorial transcription logic. Proc. Natl Acad. Sci. 100 (2003) 5136-5141
    • (2003) Proc. Natl Acad. Sci. , vol.100 , pp. 5136-5141
    • Buchler, N.E.1    Gerland, U.2    Hwa, T.3
  • 4
    • 3242881125 scopus 로고    scopus 로고
    • Responsiveness to acidity via metal ion regulators mediates virulence in the gastric pathogen Helicobacter pylori
    • Bury-Moné S., Thiberge J.-M., Contreras M., Maitournam A., Labigne A., and DeReuse H. Responsiveness to acidity via metal ion regulators mediates virulence in the gastric pathogen Helicobacter pylori. Mol. Microbiol. 53 (2004) 623-638
    • (2004) Mol. Microbiol. , vol.53 , pp. 623-638
    • Bury-Moné, S.1    Thiberge, J.-M.2    Contreras, M.3    Maitournam, A.4    Labigne, A.5    DeReuse, H.6
  • 5
    • 0042065267 scopus 로고    scopus 로고
    • Characterization of the roles of NikR, a nickel-responsive pleiotropic autoregulator of Helicobacter pylori
    • Contreras M., Thiberge J.-M., Mandrand-Berthelot M.-A., and Labigne A. Characterization of the roles of NikR, a nickel-responsive pleiotropic autoregulator of Helicobacter pylori. Mol. Microbiol. 49 (2003) 947-963
    • (2003) Mol. Microbiol. , vol.49 , pp. 947-963
    • Contreras, M.1    Thiberge, J.-M.2    Mandrand-Berthelot, M.-A.3    Labigne, A.4
  • 6
    • 27744481253 scopus 로고    scopus 로고
    • In vitro analysis of protein-operator interactions of the NikR and Fur metal-responsive regulators of coregulated genes in Helicobacter pylori
    • Delany I., Ieva R., Soragni A., Hilleringmann M., Rappuoli R., and Scarlato V. In vitro analysis of protein-operator interactions of the NikR and Fur metal-responsive regulators of coregulated genes in Helicobacter pylori. J. Bacteriol. 187 (2005) 7703-7715
    • (2005) J. Bacteriol. , vol.187 , pp. 7703-7715
    • Delany, I.1    Ieva, R.2    Soragni, A.3    Hilleringmann, M.4    Rappuoli, R.5    Scarlato, V.6
  • 7
    • 0035724513 scopus 로고    scopus 로고
    • The Fur repressor controls transcription of iron-activated and -repressed genes in Helicobacter pylori
    • Delany I., Spohn G., Rappuoli R., and Scarlato V. The Fur repressor controls transcription of iron-activated and -repressed genes in Helicobacter pylori. Mol. Microbiol. 42 (2001) 1297-1309
    • (2001) Mol. Microbiol. , vol.42 , pp. 1297-1309
    • Delany, I.1    Spohn, G.2    Rappuoli, R.3    Scarlato, V.4
  • 8
    • 29644439241 scopus 로고    scopus 로고
    • Iron and pH homeostasis intersect at the level of Fur regulation in the gastric pathogen Helicobacter pylori
    • Gancz H., Censini S., and Merrell D.S. Iron and pH homeostasis intersect at the level of Fur regulation in the gastric pathogen Helicobacter pylori. Infect. Immun. 74 (2006) 602-614
    • (2006) Infect. Immun. , vol.74 , pp. 602-614
    • Gancz, H.1    Censini, S.2    Merrell, D.S.3
  • 9
    • 0015609281 scopus 로고
    • The logical analysis of continuous, non-linear biochemical control networks
    • Glass L., and Kauffman S.A. The logical analysis of continuous, non-linear biochemical control networks. J. Theor. Biol. 39 (1973) 103-129
    • (1973) J. Theor. Biol. , vol.39 , pp. 103-129
    • Glass, L.1    Kauffman, S.A.2
  • 10
    • 39649115502 scopus 로고    scopus 로고
    • Hirsch, P., Bernhard, M., Cohen, S.S., Ensign, J.C., Jannasch, H.W., Koch, A.I., Marshall, K.C., Matin, A., Poindexter, J.S., Rittenberg, S.C., Smith, D.C., Veldkamp, H., 1979. Life under conditions of low nutrient concentrations. Group Report, pp. 357-372. In: Shio, M. (Ed.), Strategies of Microbial Life in Extreme Environments. Dahlem Konferenzen, Berlin, Germany.
    • Hirsch, P., Bernhard, M., Cohen, S.S., Ensign, J.C., Jannasch, H.W., Koch, A.I., Marshall, K.C., Matin, A., Poindexter, J.S., Rittenberg, S.C., Smith, D.C., Veldkamp, H., 1979. Life under conditions of low nutrient concentrations. Group Report, pp. 357-372. In: Shio, M. (Ed.), Strategies of Microbial Life in Extreme Environments. Dahlem Konferenzen, Berlin, Germany.
  • 12
    • 1342325451 scopus 로고    scopus 로고
    • Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media
    • Hottes A.K., Meewan M., Yang D., Arana N., Romero P., McAdams H.H., and Stephens C. Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media. J. Bacteriol. 186 (2004) 1448-1461
    • (2004) J. Bacteriol. , vol.186 , pp. 1448-1461
    • Hottes, A.K.1    Meewan, M.2    Yang, D.3    Arana, N.4    Romero, P.5    McAdams, H.H.6    Stephens, C.7
  • 13
    • 0034614490 scopus 로고    scopus 로고
    • Signaling-2000 and beyond
    • Hunter T. Signaling-2000 and beyond. Cell 100 (2000) 113-127
    • (2000) Cell , vol.100 , pp. 113-127
    • Hunter, T.1
  • 14
    • 0030089476 scopus 로고    scopus 로고
    • Mechanism responsible for glucose-lactose diauxie in Escherichia coli: challenge to the cAMP model
    • Inada T., Kimata K., and Aiba H. Mechanism responsible for glucose-lactose diauxie in Escherichia coli: challenge to the cAMP model. Genes Cells 1 (1996) 293-301
    • (1996) Genes Cells , vol.1 , pp. 293-301
    • Inada, T.1    Kimata, K.2    Aiba, H.3
  • 15
    • 17044396348 scopus 로고    scopus 로고
    • Logic functions of the genomic cis-regulatory code
    • Istrail S., and Davidson H. Logic functions of the genomic cis-regulatory code. Proc. Natl Acad. Sci. 102 (2005) 4954-4959
    • (2005) Proc. Natl Acad. Sci. , vol.102 , pp. 4954-4959
    • Istrail, S.1    Davidson, H.2
  • 17
    • 34548803596 scopus 로고    scopus 로고
    • Stochastic approach to molecular interactions and computational theory of metabolic and genetic regulations
    • Kimura H., Okano H., and Tanaka R.J. Stochastic approach to molecular interactions and computational theory of metabolic and genetic regulations. J. Theor. Biol. 248 (2007) 590-607
    • (2007) J. Theor. Biol. , vol.248 , pp. 590-607
    • Kimura, H.1    Okano, H.2    Tanaka, R.J.3
  • 21
    • 0021237174 scopus 로고
    • Conditional inversion of the thermoresponse in Escherichia coli
    • Mizuno T., and Imae Y. Conditional inversion of the thermoresponse in Escherichia coli. J. Bacteriol. 159 (1984) 360-367
    • (1984) J. Bacteriol. , vol.159 , pp. 360-367
    • Mizuno, T.1    Imae, Y.2
  • 22
    • 22444436489 scopus 로고    scopus 로고
    • An analytical study of the number of steady states in gene regulatory networks
    • Mochizuki A. An analytical study of the number of steady states in gene regulatory networks. J. Theor. Biol. 236 (2005) 291-310
    • (2005) J. Theor. Biol. , vol.236 , pp. 291-310
    • Mochizuki, A.1
  • 25
    • 0029893938 scopus 로고    scopus 로고
    • Modulation of the thermosensing profile of the Escherichia coli aspartate receptor Tar by covalent modification of its methyl-accepting sites
    • Nara T., Kawagishi I., Nishiyama S., Homma M., and Imae Y. Modulation of the thermosensing profile of the Escherichia coli aspartate receptor Tar by covalent modification of its methyl-accepting sites. J. Biol. Chem. 271 (1996) 17932-17936
    • (1996) J. Biol. Chem. , vol.271 , pp. 17932-17936
    • Nara, T.1    Kawagishi, I.2    Nishiyama, S.3    Homma, M.4    Imae, Y.5
  • 27
    • 39649091752 scopus 로고    scopus 로고
    • Neidhardt, F.C., Savageau, M.A., 1996. Regulation beyond the operon, In: Neidhardt, F.C. (Ed. in chief), Escherichia coli and Salmonella, second ed. ASM Press, Washington, DC.
    • Neidhardt, F.C., Savageau, M.A., 1996. Regulation beyond the operon, In: Neidhardt, F.C. (Ed. in chief), Escherichia coli and Salmonella, second ed. ASM Press, Washington, DC.
  • 28
    • 0345677855 scopus 로고    scopus 로고
    • Conversion of a bacterial warm sensor to a cold sensor by methylation of a single residue in the presence of an attractant
    • Nishiyama S., Umemura T., Nara T., Homma M., and Kawagishi I. Conversion of a bacterial warm sensor to a cold sensor by methylation of a single residue in the presence of an attractant. Mol. Microbiol. 32 (1999) 357-365
    • (1999) Mol. Microbiol. , vol.32 , pp. 357-365
    • Nishiyama, S.1    Umemura, T.2    Nara, T.3    Homma, M.4    Kawagishi, I.5
  • 29
    • 1442335464 scopus 로고    scopus 로고
    • Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk
    • Papin J.A., and Palsson B.O. Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. J. Theor. Biol. 227 (2004) 283-297
    • (2004) J. Theor. Biol. , vol.227 , pp. 283-297
    • Papin, J.A.1    Palsson, B.O.2
  • 30
    • 17344362384 scopus 로고    scopus 로고
    • Prediction and validation of the distinct dynamics of transient and sustained ERK activation
    • Sasagawa S., Ozaki Y., Fujita K., and Kuroda S. Prediction and validation of the distinct dynamics of transient and sustained ERK activation. Nat. Cell Biol. 7 (2005) 365-373
    • (2005) Nat. Cell Biol. , vol.7 , pp. 365-373
    • Sasagawa, S.1    Ozaki, Y.2    Fujita, K.3    Kuroda, S.4
  • 31
    • 0035578429 scopus 로고    scopus 로고
    • Design principles for elementary gene circuits: elements, methods, and examples
    • Savageau M.A. Design principles for elementary gene circuits: elements, methods, and examples. Chaos 11 (2001) 142-159
    • (2001) Chaos , vol.11 , pp. 142-159
    • Savageau, M.A.1
  • 32
    • 0032910337 scopus 로고    scopus 로고
    • Interactions between mitogenic stimuli, or, a thousand and one connections
    • Schwartz M.A., and Baron V. Interactions between mitogenic stimuli, or, a thousand and one connections. Curr. Opinion Cell Biol. 11 (1999) 197-202
    • (1999) Curr. Opinion Cell Biol. , vol.11 , pp. 197-202
    • Schwartz, M.A.1    Baron, V.2
  • 34
    • 20344374720 scopus 로고    scopus 로고
    • Bacillus subtilis ilvB operon: an intersection of global regulons
    • Shivers R.P., and Sonenshein A.L. Bacillus subtilis ilvB operon: an intersection of global regulons. Mol. Microbiol. 56 (2005) 1549-1559
    • (2005) Mol. Microbiol. , vol.56 , pp. 1549-1559
    • Shivers, R.P.1    Sonenshein, A.L.2
  • 35
    • 33846045536 scopus 로고    scopus 로고
    • Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironments
    • Soen Y., Mori A., Palmer T.D., and Brown P.O. Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironments. Mol. Syst. Biol. 2 (2006) E1-E14
    • (2006) Mol. Syst. Biol. , vol.2
    • Soen, Y.1    Mori, A.2    Palmer, T.D.3    Brown, P.O.4
  • 37
    • 33746821537 scopus 로고    scopus 로고
    • Mathematical description of gene regulatory units
    • Tanaka R.J., Okano H., and Kimura H. Mathematical description of gene regulatory units. Biophys. J. 91 (2006) 1235-1247
    • (2006) Biophys. J. , vol.91 , pp. 1235-1247
    • Tanaka, R.J.1    Okano, H.2    Kimura, H.3
  • 38
    • 0015823097 scopus 로고
    • Boolean formalization of genetic control circuits
    • Thomas R. Boolean formalization of genetic control circuits. J. Theor. Biol. 42 (1973) 563-585
    • (1973) J. Theor. Biol. , vol.42 , pp. 563-585
    • Thomas, R.1
  • 39
    • 20344400380 scopus 로고    scopus 로고
    • Elaborate transcription regulation of the Bacillus subtilis ilv-leu operon involved in the biosynthesis of branched-chain amino acids through global regulators of CcpA, CodY and TnrA
    • Tojo S., Satomura T., Morisaki K., Deutscher J., Hirooka K., and Fujita Y. Elaborate transcription regulation of the Bacillus subtilis ilv-leu operon involved in the biosynthesis of branched-chain amino acids through global regulators of CcpA, CodY and TnrA. Mol. Microbiol. 56 (2005) 1560-1573
    • (2005) Mol. Microbiol. , vol.56 , pp. 1560-1573
    • Tojo, S.1    Satomura, T.2    Morisaki, K.3    Deutscher, J.4    Hirooka, K.5    Fujita, Y.6
  • 40
    • 5644252852 scopus 로고    scopus 로고
    • NikR-mediated regulation of Helicobacter pylori acid adaptation
    • van Vilet A.H.M., Ernst F.D., and Kusters J.G. NikR-mediated regulation of Helicobacter pylori acid adaptation. Trends Microbiol. 12 (2004) 489-494
    • (2004) Trends Microbiol. , vol.12 , pp. 489-494
    • van Vilet, A.H.M.1    Ernst, F.D.2    Kusters, J.G.3
  • 41
    • 0842305636 scopus 로고    scopus 로고
    • Acid-responsive gene induction of ammonia-producing enzymes in Helicobacter pylori is mediated via a metal-responsive repressor cascade
    • van Vilet A.H.M., Kuipers E.J., Stoof J., Poppelaars S.W., and Kusters J.G. Acid-responsive gene induction of ammonia-producing enzymes in Helicobacter pylori is mediated via a metal-responsive repressor cascade. Infect. Immun. 72 (2004) 766-773
    • (2004) Infect. Immun. , vol.72 , pp. 766-773
    • van Vilet, A.H.M.1    Kuipers, E.J.2    Stoof, J.3    Poppelaars, S.W.4    Kusters, J.G.5
  • 42
    • 0032549745 scopus 로고    scopus 로고
    • Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene
    • Yuh C.-H., Bolouri H., and Davidson E.H. Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 279 (1998) 1896-1902
    • (1998) Science , vol.279 , pp. 1896-1902
    • Yuh, C.-H.1    Bolouri, H.2    Davidson, E.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.