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Volumn 56, Issue 417, 2005, Pages 1887-1896

Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response

Author keywords

Auxin; Causality; Metabolome; Network; Network topology; Plait concept; Scale free network; Sulphur metabolism; Systems biology; Transcriptome

Indexed keywords

FLUXES; METABOLITES; PERTURBATION TECHNIQUES; PHYSIOLOGY; STRESSES; SULFUR COMPOUNDS; TIME SERIES ANALYSIS; TOPOLOGY;

EID: 21344452782     PISSN: 00220957     EISSN: None     Source Type: Journal    
DOI: 10.1093/jxb/eri179     Document Type: Article
Times cited : (114)

References (51)
  • 1
    • 0034721164 scopus 로고    scopus 로고
    • Error and attack tolerance of complex networks
    • Albert R, Jeong H, Barabasi AL. 2000. Error and attack tolerance of complex networks. Nature 406, 378-382.
    • (2000) Nature , vol.406 , pp. 378-382
    • Albert, R.1    Jeong, H.2    Barabasi, A.L.3
  • 2
    • 0037316031 scopus 로고    scopus 로고
    • Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains
    • Askenazi M, Driggers EM, Holtzman DA, et al. 2003. Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains. Nature Biotechnology 21, 150-156.
    • (2003) Nature Biotechnology , vol.21 , pp. 150-156
    • Askenazi, M.1    Driggers, E.M.2    Holtzman, D.A.3
  • 3
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • Barabasi AL, Albert R. 1999. Emergence of scaling in random networks. Science 286, 509-512.
    • (1999) Science , vol.286 , pp. 509-512
    • Barabasi, A.L.1    Albert, R.2
  • 4
    • 0002226683 scopus 로고    scopus 로고
    • Pajek - Program for Large Network Analysis
    • Batagelj V, Mrvar A. 1998. Pajek - Program for Large Network Analysis. Connections 21, 47-57.
    • (1998) Connections , vol.21 , pp. 47-57
    • Batagelj, V.1    Mrvar, A.2
  • 6
    • 0034212418 scopus 로고    scopus 로고
    • The role of calcium and activated oxygens as signals for controlling cross-tolerance
    • Bowler C, Fluhr R. 2000. The role of calcium and activated oxygens as signals for controlling cross-tolerance. Trends in Plant Science 5, 241-246.
    • (2000) Trends in Plant Science , vol.5 , pp. 241-246
    • Bowler, C.1    Fluhr, R.2
  • 7
    • 0000552986 scopus 로고    scopus 로고
    • Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements
    • Butte AJ, Kohane IS. 2000. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pacific Symposium on Biocomputing 5, 415-426.
    • (2000) Pacific Symposium on Biocomputing , vol.5 , pp. 415-426
    • Butte, A.J.1    Kohane, I.S.2
  • 8
    • 0345899346 scopus 로고    scopus 로고
    • Developmentally regulated expression of the rice calmodulin promoter in transgenic tobacco plants
    • Choi YJ, Cho EK, Lee SI, Lim CO, Gal SW, Cho MJ, An GH. 1996. Developmentally regulated expression of the rice calmodulin promoter in transgenic tobacco plants. Molecular Cell 6, 541-546.
    • (1996) Molecular Cell , vol.6 , pp. 541-546
    • Choi, Y.J.1    Cho, E.K.2    Lee, S.I.3    Lim, C.O.4    Gal, S.W.5    Cho, M.J.6    An, G.H.7
  • 9
    • 0036395157 scopus 로고    scopus 로고
    • Genetic network identification by high density, multiplexed reversed transcriptional (HD-MRT) analysis in steroidogenic axis model cell lines
    • Clipsham R, Zhang YH, Huang BL, McCabe ERB. 2002. Genetic network identification by high density, multiplexed reversed transcriptional (HD-MRT) analysis in steroidogenic axis model cell lines. Molecular Genetics and Metabolism 77, 159-178.
    • (2002) Molecular Genetics and Metabolism , vol.77 , pp. 159-178
    • Clipsham, R.1    Zhang, Y.H.2    Huang, B.L.3    McCabe, E.R.B.4
  • 10
    • 0002684378 scopus 로고    scopus 로고
    • Amino acids
    • Buchanan BB, Gruissem W, Jones RL, eds. Rockville, Maryland: American Society of Plant Physiologists
    • Coruzzi G, Last R. 2000. Amino acids. In: Buchanan BB, Gruissem W, Jones RL, eds. Biochemistry and molecular biology of plants. Rockville, Maryland: American Society of Plant Physiologists, 358-410.
    • (2000) Biochemistry and Molecular Biology of Plants , pp. 358-410
    • Coruzzi, G.1    Last, R.2
  • 11
    • 0344464731 scopus 로고    scopus 로고
    • MetaGeneAlyse: Analysis of integrated transcriptional and metabolite data
    • Daub CO, Kloska S, Selbig J. 2003. MetaGeneAlyse: analysis of integrated transcriptional and metabolite data. Bioinformatics 19, 2332-2333.
    • (2003) Bioinformatics , vol.19 , pp. 2332-2333
    • Daub, C.O.1    Kloska, S.2    Selbig, J.3
  • 12
    • 13244267007 scopus 로고    scopus 로고
    • Estimating mutual information using B-spline functions: An improved similarity measure for analysing gene expression data
    • Daub CO, Steuer R, Selbig J, Kloska S. 2004. Estimating mutual information using B-spline functions: an improved similarity measure for analysing gene expression data. BMC Bioinformatics 5, 118.
    • (2004) BMC Bioinformatics , vol.5 , pp. 118
    • Daub, C.O.1    Steuer, R.2    Selbig, J.3    Kloska, S.4
  • 13
    • 0034625143 scopus 로고    scopus 로고
    • The Escherichia coli MG1655 in silica metabolic genotype: Its definition, characteristics, and capabilities
    • Edwards JS, Palsson BO. 2000. The Escherichia coli MG1655 in silica metabolic genotype: its definition, characteristics, and capabilities. Proceedings of the National Academy of Sciences, USA 97, 5528-5533.
    • (2000) Proceedings of the National Academy of Sciences, USA , vol.97 , pp. 5528-5533
    • Edwards, J.S.1    Palsson, B.O.2
  • 15
    • 0036006175 scopus 로고    scopus 로고
    • Wrestling with pleiotropy: Genomic and topological analysis of the yeast gene expression network
    • Featherstone DE, Broadie K. 2002. Wrestling with pleiotropy: genomic and topological analysis of the yeast gene expression network. Bioessays 24, 267-274.
    • (2002) Bioessays , vol.24 , pp. 267-274
    • Featherstone, D.E.1    Broadie, K.2
  • 16
    • 7144261208 scopus 로고
    • Auxin causes oscillations of cytosolic free calcium and pH in Zea mays coleoptiles
    • Felle H. 1988. Auxin causes oscillations of cytosolic free calcium and pH in Zea mays coleoptiles. Planta 174, 495-499.
    • (1988) Planta , vol.174 , pp. 495-499
    • Felle, H.1
  • 18
    • 0013790723 scopus 로고
    • Synthesis of the succinic ester of homoserine, a new intermediate in the bacterial biosynthesis of methionine
    • Flavin M, Slaughter C. 1965. Synthesis of the succinic ester of homoserine, a new intermediate in the bacterial biosynthesis of methionine. Biochemistry 4, 1370-1375.
    • (1965) Biochemistry , vol.4 , pp. 1370-1375
    • Flavin, M.1    Slaughter, C.2
  • 19
    • 0036709912 scopus 로고    scopus 로고
    • Network genomics: A novel approach for the analysis of biological systems in the post-genomic era
    • Forst CV. 2002. Network genomics: a novel approach for the analysis of biological systems in the post-genomic era. Molecular Biology Reporter 29, 265-280.
    • (2002) Molecular Biology Reporter , vol.29 , pp. 265-280
    • Forst, C.V.1
  • 21
    • 0345504891 scopus 로고    scopus 로고
    • Crosstalk in plant cell signalling: Structure and function of the genetic network
    • Genoud T, Metraux JP. 1999. Crosstalk in plant cell signalling: structure and function of the genetic network. Trends in Plant Science 4, 503-507.
    • (1999) Trends in Plant Science , vol.4 , pp. 503-507
    • Genoud, T.1    Metraux, J.P.2
  • 22
    • 0037249405 scopus 로고    scopus 로고
    • The Stanford microarray database: Data access and quality assessment tools
    • Gollub J, Ball CA, Binkley G, et al. 2003. The Stanford microarray database: data access and quality assessment tools. Nucleic Acids Research 31, 94-96.
    • (2003) Nucleic Acids Research , vol.31 , pp. 94-96
    • Gollub, J.1    Ball, C.A.2    Binkley, G.3
  • 23
    • 0036061833 scopus 로고    scopus 로고
    • Pathway processor: A tool for integrating whole-genome expression results into metabolic networks
    • Grosu P, Townsend JP, Hartl DL, Cavalieri D. 2002. Pathway processor: a tool for integrating whole-genome expression results into metabolic networks. Genome Research 12, 1121-1126.
    • (2002) Genome Research , vol.12 , pp. 1121-1126
    • Grosu, P.1    Townsend, J.P.2    Hartl, D.L.3    Cavalieri, D.4
  • 24
    • 0032473570 scopus 로고    scopus 로고
    • The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development
    • Hardtke CS, Berleth T. 1998. The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development. EMBO Journal 17, 1405-1411.
    • (1998) EMBO Journal , vol.17 , pp. 1405-1411
    • Hardtke, C.S.1    Berleth, T.2
  • 25
    • 0344177200 scopus 로고    scopus 로고
    • Global expression profiling of sulfur-starved Arabidopsis by DNA macroarray reveals the role of O-acetyl-L-serine as a general regulator of gene expression in response to sulfur nutrition
    • Hirai MY, Fujiwara T, Awazuhara M, Kimura T, Noji M, Saito K. 2003. Global expression profiling of sulfur-starved Arabidopsis by DNA macroarray reveals the role of O-acetyl-L-serine as a general regulator of gene expression in response to sulfur nutrition. The Plant Journal 33, 651-663.
    • (2003) The Plant Journal , vol.33 , pp. 651-663
    • Hirai, M.Y.1    Fujiwara, T.2    Awazuhara, M.3    Kimura, T.4    Noji, M.5    Saito, K.6
  • 28
    • 0042595754 scopus 로고    scopus 로고
    • Distribution of membrane-bound calcium and activated calmodulin in cultured protoplasts of sunflower (Helianthus annum L)
    • Kalra G, Bhatla SC. 1999. Distribution of membrane-bound calcium and activated calmodulin in cultured protoplasts of sunflower (Helianthus annum L). Current Science 76, 1580-1584.
    • (1999) Current Science , vol.76 , pp. 1580-1584
    • Kalra, G.1    Bhatla, S.C.2
  • 29
    • 0035820191 scopus 로고    scopus 로고
    • Cybernetic formulation of the definition of life
    • Korzeniewski B. 2001. Cybernetic formulation of the definition of life. Journal of Theoretical Biology 209, 275-286.
    • (2001) Journal of Theoretical Biology , vol.209 , pp. 275-286
    • Korzeniewski, B.1
  • 30
    • 0036011031 scopus 로고    scopus 로고
    • A role for nitrilase 3 in the regulation of root morphology in sulphur-starving Arabidopsis thaliana
    • Kutz A, Müller A, Hennig P, Kaiser WM, Piotrowski M, Weiler EW. 2002. A role for nitrilase 3 in the regulation of root morphology in sulphur-starving Arabidopsis thaliana. The Plant Journal 30, 95-106.
    • (2002) The Plant Journal , vol.30 , pp. 95-106
    • Kutz, A.1    Müller, A.2    Hennig, P.3    Kaiser, W.M.4    Piotrowski, M.5    Weiler, E.W.6
  • 32
    • 0035193510 scopus 로고    scopus 로고
    • Environmental regulation of lateral root initiation in Arabidopsis
    • Malamy JE, Ryan KS. 2001. Environmental regulation of lateral root initiation in Arabidopsis. Plant Physiology 127, 899-909.
    • (2001) Plant Physiology , vol.127 , pp. 899-909
    • Malamy, J.E.1    Ryan, K.S.2
  • 33
    • 0036148354 scopus 로고    scopus 로고
    • Vulnerability within a robust complex system-DAX-1 mutations and steroidogenic axis development
    • McCabe ERB. 2002. Vulnerability within a robust complex system-DAX-1 mutations and steroidogenic axis development. Journal of Clinical Endocrinology and Metabolism 87, 41-43.
    • (2002) Journal of Clinical Endocrinology and Metabolism , vol.87 , pp. 41-43
    • McCabe, E.R.B.1
  • 34
    • 0038460047 scopus 로고    scopus 로고
    • AraCyc: A biochemical pathway database for Arabidopsis
    • Mueller LA, Zhang PF, Rhee SY. 2003. AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiology 132, 453-460.
    • (2003) Plant Physiology , vol.132 , pp. 453-460
    • Mueller, L.A.1    Zhang, P.F.2    Rhee, S.Y.3
  • 35
    • 21344432822 scopus 로고
    • Involvement of calcium in brassinolide and auxin-induced cell elongation
    • Naren A, Prasad TG, Sashidhar VR, Kumar MU. 1995. Involvement of calcium in brassinolide and auxin-induced cell elongation. Current Science 69, 777-780.
    • (1995) Current Science , vol.69 , pp. 777-780
    • Naren, A.1    Prasad, T.G.2    Sashidhar, V.R.3    Kumar, M.U.4
  • 36
    • 0037296141 scopus 로고    scopus 로고
    • Transcriptome analysis of sulfur depletion in Arabidopsis thaliana: Interlacing of biosynthetic pathways provides response specificity
    • Nikiforova V, Freitag J, Kempa S, Adamik M, Hesse H, Hoefgen R. 2003. Transcriptome analysis of sulfur depletion in Arabidopsis thaliana: interlacing of biosynthetic pathways provides response specificity. The Plant Journal 33, 633-650.
    • (2003) The Plant Journal , vol.33 , pp. 633-650
    • Nikiforova, V.1    Freitag, J.2    Kempa, S.3    Adamik, M.4    Hesse, H.5    Hoefgen, R.6
  • 38
    • 0029582863 scopus 로고
    • Molecular cloning and analysis of the cDNA for an auxin-regulated calmodulin gene
    • Okamoto H, Tanaka Y, Sakai S. 1995. Molecular cloning and analysis of the cDNA for an auxin-regulated calmodulin gene. Plant Cell Physiology 36, 1531-1539.
    • (1995) Plant Cell Physiology , vol.36 , pp. 1531-1539
    • Okamoto, H.1    Tanaka, Y.2    Sakai, S.3
  • 39
    • 0029959271 scopus 로고    scopus 로고
    • Studies on the role of the Arabidopsis gene MONOPTEROS in vascular development and plant cell axialization
    • Przemeck GKH, Mattsson J, Hardtke CS, Sung ZR, Berleth T. 1996. Studies on the role of the Arabidopsis gene MONOPTEROS in vascular development and plant cell axialization. Planta 200, 229-237.
    • (1996) Planta , vol.200 , pp. 229-237
    • Przemeck, G.K.H.1    Mattsson, J.2    Hardtke, C.S.3    Sung, Z.R.4    Berleth, T.5
  • 40
    • 0035062610 scopus 로고    scopus 로고
    • A gain-of-function mutation in IAA28 suppresses lateral root development
    • Rogg LE, Lasswell J, Bartel B. 2001. A gain-of-function mutation in IAA28 suppresses lateral root development. The Plant Cell 13, 465-480.
    • (2001) The Plant Cell , vol.13 , pp. 465-480
    • Rogg, L.E.1    Lasswell, J.2    Bartel, B.3
  • 41
    • 0036428761 scopus 로고    scopus 로고
    • Negative autoregulation speeds the response times of transcription networks
    • Rosenfeld N, Elowitz MB, Alon U. 2002. Negative autoregulation speeds the response times of transcription networks. Journal of Molecular Biology 323, 785-793.
    • (2002) Journal of Molecular Biology , vol.323 , pp. 785-793
    • Rosenfeld, N.1    Elowitz, M.B.2    Alon, U.3
  • 43
    • 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. Nature Genetics 31, 64-68.
    • (2002) Nature Genetics , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 44
    • 0037079050 scopus 로고    scopus 로고
    • Metabolic network structure determines key aspects of functionality and regulation
    • Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED. 2002. Metabolic network structure determines key aspects of functionality and regulation. Nature 420, 190-193.
    • (2002) Nature , vol.420 , pp. 190-193
    • Stelling, J.1    Klamt, S.2    Bettenbrock, K.3    Schuster, S.4    Gilles, E.D.5
  • 45
    • 0042526388 scopus 로고    scopus 로고
    • The mutual information: Detecting and evaluating dependencies between variables
    • Steuer R, Kurths J, Daub CO, Weise J, Selbig J. 2002. The mutual information: detecting and evaluating dependencies between variables. Bioinformatics 18, S231-S240.
    • (2002) Bioinformatics , vol.18
    • Steuer, R.1    Kurths, J.2    Daub, C.O.3    Weise, J.4    Selbig, J.5
  • 46
    • 0036720908 scopus 로고    scopus 로고
    • Anthocyanins in vegetative tissues: A proposed unified function in photoprotection
    • Steyn WJ, Wand SJE, Holcroft DM, Jacobs G. 2002. Anthocyanins in vegetative tissues: a proposed unified function in photoprotection. New Phytologist 155, 349-361.
    • (2002) New Phytologist , vol.155 , pp. 349-361
    • Steyn, W.J.1    Wand, S.J.E.2    Holcroft, D.M.3    Jacobs, G.4
  • 47
    • 0032077377 scopus 로고    scopus 로고
    • From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Eschherichia coli
    • Thieffry D, Huerta AM, Perezrueda E, Colladovides J. 1998. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Eschherichia coli. Bioessays 20, 433-440.
    • (1998) Bioessays , vol.20 , pp. 433-440
    • Thieffry, D.1    Huerta, A.M.2    Perezrueda, E.3    Colladovides, J.4
  • 50
    • 0034603001 scopus 로고    scopus 로고
    • Molecular and biochemical evidence for the involvement of calcium/calmodulin in auxin action
    • Yang TB, Poovaiah BW. 2000. Molecular and biochemical evidence for the involvement of calcium/calmodulin in auxin action. Journal of Biological Chemistry 275, 3137-3143.
    • (2000) Journal of Biological Chemistry , vol.275 , pp. 3137-3143
    • Yang, T.B.1    Poovaiah, B.W.2
  • 51
    • 0037160040 scopus 로고    scopus 로고
    • A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signalling pathways in plants
    • Yang TB, Poovaiah BW. 2002. A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signalling pathways in plants. Journal of Biological Chemistry 277, 45049-45058.
    • (2002) Journal of Biological Chemistry , vol.277 , pp. 45049-45058
    • Yang, T.B.1    Poovaiah, B.W.2


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