메뉴 건너뛰기




Volumn 20, Issue 12, 2004, Pages 1877-1886

Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data

Author keywords

[No Author keywords available]

Indexed keywords

MITOGEN ACTIVATED PROTEIN KINASE; MITOGEN ACTIVATED PROTEIN KINASE KINASE; RAS PROTEIN;

EID: 4444226267     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth173     Document Type: Article
Times cited : (141)

References (55)
  • 1
    • 0000122278 scopus 로고
    • Statistical construction of chemical reaction mechanisms from measured time-series
    • Arkin,A. and Ross,J. (1995) Statistical construction of chemical reaction mechanisms from measured time-series. J. Phys. Chem., 99, 970-979.
    • (1995) J. Phys. Chem. , vol.99 , pp. 970-979
    • Arkin, A.1    Ross, J.2
  • 2
    • 0030848624 scopus 로고    scopus 로고
    • A test case of correlation metric construction of a reaction pathway from measurements
    • Arkin,A., Shen,P. and Ross,J. (1997) A test case of correlation metric construction of a reaction pathway from measurements. Science, 277, 1275-1279.
    • (1997) Science , vol.277 , pp. 1275-1279
    • Arkin, A.1    Shen, P.2    Ross, J.3
  • 3
    • 0035822634 scopus 로고    scopus 로고
    • Bistability in the JNK cascade
    • Bagowski,C.P. and Ferrell,J.E.,Jr. (2001) Bistability in the JNK cascade. Curr. Biol., 11, 1176-1182.
    • (2001) Curr. Biol. , vol.11 , pp. 1176-1182
    • Bagowski, C.P.1    Ferrell Jr., J.E.2
  • 4
    • 0036856356 scopus 로고    scopus 로고
    • A duplication growth model of gene expression networks
    • Bhan,A., Galas,D.J. and Dewey,T.G. (2002) A duplication growth model of gene expression networks. Bioinformatics, 18, 1486-1493.
    • (2002) Bioinformatics , vol.18 , pp. 1486-1493
    • Bhan, A.1    Galas, D.J.2    Dewey, T.G.3
  • 5
    • 0031203337 scopus 로고    scopus 로고
    • Why do protein kinase cascades have more than one level?
    • Brown,G.C., Hoek,J.B. and Kholodenko,B.N. (1997) Why do protein kinase cascades have more than one level? Trends Biochem. Sci., 22, 288.
    • (1997) Trends Biochem. Sci. , vol.22 , pp. 288
    • Brown, G.C.1    Hoek, J.B.2    Kholodenko, B.N.3
  • 8
    • 0024673575 scopus 로고
    • Use of implicit methods from general sensitivity theory to develop a systematic approach to metabolic control. II. Complex systems
    • Cascante,M., Franco,R. and Canela,E.I. (1989) Use of implicit methods from general sensitivity theory to develop a systematic approach to metabolic control. II. Complex systems. Math. Biosci., 94, 289-309.
    • (1989) Math. Biosci. , vol.94 , pp. 289-309
    • Cascante, M.1    Franco, R.2    Canela, E.I.3
  • 9
    • 0035282334 scopus 로고    scopus 로고
    • Mammalian MAP kinase signalling cascades
    • Chang,L. and Karin,M. (2001) Mammalian MAP kinase signalling cascades. Nature, 410, 37-40.
    • (2001) Nature , vol.410 , pp. 37-40
    • Chang, L.1    Karin, M.2
  • 10
    • 0001622226 scopus 로고
    • Toward a systematic determination of complex reaction mechanisms
    • Chevalier,T., Schreiber,T. and Ross,J. (1993) Toward a systematic determination of complex reaction mechanisms. J. Phys. Chem., 97, 6776-6787.
    • (1993) J. Phys. Chem. , vol.97 , pp. 6776-6787
    • Chevalier, T.1    Schreiber, T.2    Ross, J.3
  • 11
    • 0032837252 scopus 로고    scopus 로고
    • Computational methods for the identification of differential and coordinated gene expression
    • Claverie,J.M. (1999) Computational methods for the identification of differential and coordinated gene expression. Hum. Mol. Genet., 8, 1821-1832.
    • (1999) Hum. Mol. Genet. , vol.8 , pp. 1821-1832
    • Claverie, J.M.1
  • 12
    • 0036683181 scopus 로고    scopus 로고
    • Linking the genes: Inferring quantitative gene networks from microarray data
    • de la Fuente,A., Brazhnik,P. and Mendes,P. (2002) Linking the genes: inferring quantitative gene networks from microarray data. Trends Genet., 18, 395-398.
    • (2002) Trends Genet. , vol.18 , pp. 395-398
    • de la Fuente, A.1    Brazhnik, P.2    Mendes, P.3
  • 13
    • 0033736476 scopus 로고    scopus 로고
    • Genetic network inference: From co-expression clustering to reverse engineering
    • D'Haeseleer,P., Liang,S. and Somogyi,R. (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics, 16, 707-726.
    • (2000) Bioinformatics , vol.16 , pp. 707-726
    • D'Haeseleer, P.1    Liang, S.2    Somogyi, R.3
  • 14
    • 0035125986 scopus 로고    scopus 로고
    • In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
    • Edwards,J.S., Ibarra,R.U. and Palsson,B.O. (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol., 19, 125-130.
    • (2001) Nat. Biotechnol. , vol.19 , pp. 125-130
    • Edwards, J.S.1    Ibarra, R.U.2    Palsson, B.O.3
  • 15
    • 0032496358 scopus 로고    scopus 로고
    • The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes
    • Ferrell,J.E.,Jr. and Machleder,E.M. (1998) The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science, 280, 895-898.
    • (1998) Science , vol.280 , pp. 895-898
    • Ferrell Jr., J.E.1    Machleder, E.M.2
  • 16
    • 3242882981 scopus 로고    scopus 로고
    • Chain functions and scoring functions in genetic networks
    • Gat-Viks,I. and Shamir,R. (2003) Chain functions and scoring functions in genetic networks. Bioinformatics, 19, I108-I117.
    • (2003) Bioinformatics , vol.19
    • Gat-Viks, I.1    Shamir, R.2
  • 17
    • 0026287765 scopus 로고
    • The kinetics of mammalian gene expression
    • Hargrove,J.L., Hulsey,M.G. and Beale,E.G. (1991) The kinetics of mammalian gene expression. Bioessays, 13, 667-674.
    • (1991) Bioessays , vol.13 , pp. 667-674
    • Hargrove, J.L.1    Hulsey, M.G.2    Beale, E.G.3
  • 18
    • 0344464762 scopus 로고    scopus 로고
    • Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks
    • Husmeier,D. (2003) Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. Bioinformatics, 19, 2271-2282.
    • (2003) Bioinformatics , vol.19 , pp. 2271-2282
    • Husmeier, D.1
  • 19
    • 0033642067 scopus 로고    scopus 로고
    • Discovery of regulatory interactions through perturbation: Inference and experimental design
    • Ideker,T.E., Thorsson,V. and Karp,R.M. (2000) Discovery of regulatory interactions through perturbation: inference and experimental design. Pac. Symp. Biocomput., 305-316.
    • (2000) Pac. Symp. Biocomput. , pp. 305-316
    • Ideker, T.E.1    Thorsson, V.2    Karp, R.M.3
  • 20
    • 0037466509 scopus 로고    scopus 로고
    • Sensitivity analysis of stoichiometric networks: An extension of metabolic control analysis to non-steady state trajectories
    • Ingalls,B.P. and Sauro,H.M. (2003) Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. J. Theor. Biol., 222, 23-36.
    • (2003) J. Theor. Biol. , vol.222 , pp. 23-36
    • Ingalls, B.P.1    Sauro, H.M.2
  • 21
    • 0033667580 scopus 로고    scopus 로고
    • Dynamics of gene expression in rat hepatocytes under stress
    • Jayaraman,A., Yarmush,M.L. and Roth,C.M. (2000) Dynamics of gene expression in rat hepatocytes under stress. Metab. Eng., 2, 239-251.
    • (2000) Metab. Eng. , vol.2 , pp. 239-251
    • Jayaraman, A.1    Yarmush, M.L.2    Roth, C.M.3
  • 22
    • 0034019315 scopus 로고    scopus 로고
    • Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades
    • Kholodenko,B.N. (2000) Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem., 267, 1583-1588.
    • (2000) Eur. J. Biochem. , vol.267 , pp. 1583-1588
    • Kholodenko, B.N.1
  • 23
    • 0033570090 scopus 로고    scopus 로고
    • Quantification of short term signaling by the epidermal growth factor receptor
    • Kholodenko,B.N., Demin,O.V., Moehren,G. and Hoek,J.B. (1999) Quantification of short term signaling by the epidermal growth factor receptor. J. Biol. Chem., 274, 30169-30181.
    • (1999) J. Biol. Chem. , vol.274 , pp. 30169-30181
    • Kholodenko, B.N.1    Demin, O.V.2    Moehren, G.3    Hoek, J.B.4
  • 24
    • 0031099173 scopus 로고    scopus 로고
    • Control analysis of periodic phenomena in biological systems
    • Kholodenko,B.N., Demin,O.V. and Westerhoff,H.V. (1997a) Control analysis of periodic phenomena in biological systems. J. Phys. Chem., 101, 2070-2081.
    • (1997) J. Phys. Chem. , vol.101 , pp. 2070-2081
    • Kholodenko, B.N.1    Demin, O.V.2    Westerhoff, H.V.3
  • 25
    • 0031559933 scopus 로고    scopus 로고
    • Quantification of information transfer via cellular signal transduction pathways
    • [Erratum (1997) FEBS Lett. 419 150.]
    • Kholodenko,B.N., Hoek,J.B., Westerhoff,H.V. and Brown,G.C. (1997b) Quantification of information transfer via cellular signal transduction pathways [Erratum (1997) FEBS Lett. 419 150.] FEBS Lett., 414, 430-434.
    • (1997) FEBS Lett. , vol.414 , pp. 430-434
    • Kholodenko, B.N.1    Hoek, J.B.2    Westerhoff, H.V.3    Brown, G.C.4
  • 27
    • 3242704801 scopus 로고    scopus 로고
    • Determination of Functional Network Structure from Local Parameter Dependence Data
    • arXiv: physics/0205003
    • Kholodenko,B.N. and Sontag,E.D. (2002) Determination of Functional Network Structure from Local Parameter Dependence Data. arXiv: physics/0205003.
    • (2002)
    • Kholodenko, B.N.1    Sontag, E.D.2
  • 28
    • 0028836695 scopus 로고
    • The macroworld versus the microworld of biochemical regulation and control
    • Kholodenko,B.N. and Westerhoff,H.V. (1995) The macroworld versus the microworld of biochemical regulation and control. Trends Biochem. Sci., 20, 52-54.
    • (1995) Trends Biochem. Sci. , vol.20 , pp. 52-54
    • Kholodenko, B.N.1    Westerhoff, H.V.2
  • 29
    • 0028898474 scopus 로고
    • Control in channelled pathways. A matrix method calculating the enzyme control coefficients
    • Kholodenko,B.N., Westerhoff,H.V., Puigjaner,J. and Cascante,M. (1995) Control in channelled pathways. A matrix method calculating the enzyme control coefficients. Biophys. Chem., 53, 247-258.
    • (1995) Biophys. Chem. , vol.53 , pp. 247-258
    • Kholodenko, B.N.1    Westerhoff, H.V.2    Puigjaner, J.3    Cascante, M.4
  • 30
    • 0028829346 scopus 로고
    • Negative feedback regulation and desensitization of insulin- and epidermal growth factor-stimulated p21ras activation
    • Langlois,W.J., Sasaoka,T., Saltiel,A.R. and Olefsky,J.M. (1995) Negative feedback regulation and desensitization of insulin- and epidermal growth factor-stimulated p21ras activation. J. Biol. Chem., 270, 25320-25323.
    • (1995) J. Biol. Chem. , vol.270 , pp. 25320-25323
    • Langlois, W.J.1    Sasaoka, T.2    Saltiel, A.R.3    Olefsky, J.M.4
  • 32
    • 0034705227 scopus 로고    scopus 로고
    • Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties
    • Levchenko,A., Bruck,J. and Sternberg,P.W. (2000) Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc. Natl Acad. Sci., USA, 97, 5818-5823.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 5818-5823
    • Levchenko, A.1    Bruck, J.2    Sternberg, P.W.3
  • 35
    • 0037039289 scopus 로고    scopus 로고
    • Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model
    • Moehren,G., Markevich,N., Demin,O., Kiyatkin,A., Goryanin,I., Hoek,J.B. and Kholodenko,B.N. (2002) Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model. Biochemistry, 41, 306-320.
    • (2002) Biochemistry , vol.41 , pp. 306-320
    • Moehren, G.1    Markevich, N.2    Demin, O.3    Kiyatkin, A.4    Goryanin, I.5    Hoek, J.B.6    Kholodenko, B.N.7
  • 36
    • 0033518256 scopus 로고    scopus 로고
    • Synexpression groups in eukaryotes
    • Niehrs,C. and Pollet,N. (1999) Synexpression groups in eukaryotes. Nature, 402, 483-487.
    • (1999) Nature , vol.402 , pp. 483-487
    • Niehrs, C.1    Pollet, N.2
  • 37
    • 0028897360 scopus 로고
    • Mechanism of eve stripe formation
    • Reinitz,J. and Sharp,D.H. (1995) Mechanism of eve stripe formation. Mech. Dev., 49, 133-158.
    • (1995) Mech. Dev. , vol.49 , pp. 133-158
    • Reinitz, J.1    Sharp, D.H.2
  • 38
    • 0036627676 scopus 로고    scopus 로고
    • Reverse engineering of regulatory networks: Simulation studies on a genetic algorithm approach for ranking hypotheses
    • Repsilber,D., Liljenstrom,H. and Andersson,S.G.E. (2002) Reverse engineering of regulatory networks: simulation studies on a genetic algorithm approach for ranking hypotheses. Biosystems, 66, 31-41.
    • (2002) Biosystems , vol.66 , pp. 31-41
    • Repsilber, D.1    Liljenstrom, H.2    Andersson, S.G.E.3
  • 40
    • 0041744850 scopus 로고    scopus 로고
    • On the deduction of chemical reaction pathways from measurements of time series of concentrations
    • Samoilov,M., Arkin,A. and Ross,J. (2001) On the deduction of chemical reaction pathways from measurements of time series of concentrations. Chaos, 11, 108-114.
    • (2001) Chaos , vol.11 , pp. 108-114
    • Samoilov, M.1    Arkin, A.2    Ross, J.3
  • 41
    • 0036212767 scopus 로고    scopus 로고
    • Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors
    • Schoeberl, B., Eichler-Jonsson,C., Gilles,E.D. and Muller,G. (2002) Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat. Biotechnol., 20, 370-375.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 370-375
    • Schoeberl, B.1    Eichler-Jonsson, C.2    Gilles, E.D.3    Muller, G.4
  • 42
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • Schuster,S., Fell,D.A. and Dandekar,T. (2000) A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol., 18, 326-332.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 326-332
    • Schuster, S.1    Fell, D.A.2    Dandekar, T.3
  • 44
    • 0038094430 scopus 로고    scopus 로고
    • From the top down: Towards a predictive biology of signalling networks
    • Stark,J., Callard,R. and Hubank,M. (2003) From the top down: towards a predictive biology of signalling networks. Trends Biotechnol., 21, 290-293.
    • (2003) Trends Biotechnol. , vol.21 , pp. 290-293
    • Stark, J.1    Callard, R.2    Hubank, M.3
  • 45
    • 0037687416 scopus 로고    scopus 로고
    • Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
    • Tegner,J., Yeung,M.K., Hasty,J. and Collins,J.J. (2003) Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc. Natl Acad. Sci., USA, 100, 5944-5949.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 5944-5949
    • Tegner, J.1    Yeung, M.K.2    Hasty, J.3    Collins, J.J.4
  • 46
    • 36749108213 scopus 로고
    • Classification of instabilities in chemical reaction systems
    • Tyson,J.J. (1975) Classification of instabilities in chemical reaction systems. J. Chem. Phys., 62, 1010-1015.
    • (1975) J. Chem. Phys. , vol.62 , pp. 1010-1015
    • Tyson, J.J.1
  • 49
    • 0037197832 scopus 로고    scopus 로고
    • Determination of causal connectivities of species in reaction networks
    • Vance,W., Arkin,A. and Ross,J. (2002) Determination of causal connectivities of species in reaction networks. Proc. Natl Acad. Sci., USA, 99, 5816-5821.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 5816-5821
    • Vance, W.1    Arkin, A.2    Ross, J.3
  • 50
    • 0034644270 scopus 로고    scopus 로고
    • The segment polarity network is a robust developmental module
    • von Dassow,G., Meir,E., Munro,E.M. and Odell,G.M. (2000) The segment polarity network is a robust developmental module. Nature, 406, 188-192.
    • (2000) Nature , vol.406 , pp. 188-192
    • von Dassow, G.1    Meir, E.2    Munro, E.M.3    Odell, G.M.4
  • 51
    • 0034104824 scopus 로고    scopus 로고
    • Coarse-grained reverse engineering of genetic regulatory networks
    • Wahde,M. and Hertz,J. (2000) Coarse-grained reverse engineering of genetic regulatory networks. Biosystems, 55, 129-136.
    • (2000) Biosystems , vol.55 , pp. 129-136
    • Wahde, M.1    Hertz, J.2
  • 52
    • 0028234589 scopus 로고
    • Getting to the inside of cells using metabolic control analysis
    • Westerhoff,H.V., Hofmeyr,J.H. and Kholodenko,B.N. (1994) Getting to the inside of cells using metabolic control analysis. Biophys. Chem., 50, 273-283.
    • (1994) Biophys. Chem. , vol.50 , pp. 273-283
    • Westerhoff, H.V.1    Hofmeyr, J.H.2    Kholodenko, B.N.3
  • 53
    • 0141925279 scopus 로고    scopus 로고
    • Process pathway inference via time series analysis
    • Wiggins,C. and Nemenman,I. (2003) Process pathway inference via time series analysis. Exp. Mechan., 43, 361-370.
    • (2003) Exp. Mechan. , vol.43 , pp. 361-370
    • Wiggins, C.1    Nemenman, I.2
  • 54
    • 0037197936 scopus 로고    scopus 로고
    • Reverse engineering gene networks using singular value decomposition and robust regression
    • Yeung,M.K., Tegner,J. and Collins,J.J. (2002) Reverse engineering gene networks using singular value decomposition and robust regression. Proc. Natl Acad. Sci., USA, 99, 6163-6168.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 6163-6168
    • Yeung, M.K.1    Tegner, J.2    Collins, J.J.3
  • 55
    • 0037205479 scopus 로고    scopus 로고
    • ERK negatively regulates the epidermal growth factor-mediated interaction of Gab 1 and the phosphatidylinositol 3-kinase
    • Yu,C.F., Liu,Z.X. and Cantley,L.G. (2002) ERK negatively regulates the epidermal growth factor-mediated interaction of Gab 1 and the phosphatidylinositol 3-kinase. J. Biol. Chem., 277, 19382-19388.
    • (2002) J. Biol. Chem. , vol.277 , pp. 19382-19388
    • Yu, C.F.1    Liu, Z.X.2    Cantley, L.G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.