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Volumn 10, Issue 7, 2014, Pages

Minimal metabolic pathway structure is consistent with associated biomolecular interactions

Author keywords

constraint based modeling; genetic interactions; pathway analysis; protein protein interactions; transcriptional regulatory networks

Indexed keywords

CARBON; FATTY ACID; TRANSCRIPTION FACTOR; ESCHERICHIA COLI PROTEIN;

EID: 84905403664     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.15252/msb.20145243     Document Type: Article
Times cited : (38)

References (57)
  • 1
    • 77956511890 scopus 로고    scopus 로고
    • Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum
    • Amador-Noquez D, Feng XJ, Fan J, Roquet N, Rabitz H, Rabinowitz JD, (2010) Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum. J Bacteriol 192: 4452-4461
    • (2010) J Bacteriol , vol.192 , pp. 4452-4461
    • Amador-Noquez, D.1    Feng, X.J.2    Fan, J.3    Roquet, N.4    Rabitz, H.5    Rabinowitz, J.D.6
  • 6
    • 0014980473 scopus 로고
    • Catabolite repression of tryptophanase in Escherichia coli
    • Botsford JL, DeMoss RD, (1971) Catabolite repression of tryptophanase in Escherichia coli. J Bacteriol 105: 303-312
    • (1971) J Bacteriol , vol.105 , pp. 303-312
    • Botsford, J.L.1    Demoss, R.D.2
  • 11
    • 0002013127 scopus 로고
    • Stability of complex reaction networks
    • Rice IPASA (ed.), New York: John Wiley
    • Clarke BL, (1980). Stability of complex reaction networks. In Advances in Chemical Physics, Rice IPASA, (ed.), pp. 1-215. New York: John Wiley
    • (1980) Advances in Chemical Physics , pp. 1-215
    • Clarke, B.L.1
  • 12
    • 0000023441 scopus 로고
    • The null space problem I. Complexity
    • Coleman TF, Pothen A, (1986) The null space problem I. Complexity. Soc Indust Appl Math 7: 527-537
    • (1986) Soc Indust Appl Math , vol.7 , pp. 527-537
    • Coleman, T.F.1    Pothen, A.2
  • 14
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • DOI 10.1038/nature02456
    • Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO, (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96 (Pubitemid 38620557)
    • (2004) Nature , vol.429 , Issue.6987 , pp. 92-96
    • Covert, M.W.1    Knight, E.M.2    Reed, J.L.3    Herrgard, M.J.4    Palsson, B.O.5
  • 15
    • 84872181616 scopus 로고    scopus 로고
    • Automating the construction of gene ontologies
    • Dolinski K, Botstein D, (2013) Automating the construction of gene ontologies. Nat Biotechnol 31: 34-35
    • (2013) Nat Biotechnol , vol.31 , pp. 34-35
    • Dolinski, K.1    Botstein, D.2
  • 20
    • 78149306565 scopus 로고    scopus 로고
    • Matrix sparsification and the sparse null space problem
    • Gottlieb L, Neylon T, (2010) Matrix sparsification and the sparse null space problem. Approx 6302: 205-218
    • (2010) Approx , vol.6302 , pp. 205-218
    • Gottlieb, L.1    Neylon, T.2
  • 21
    • 79953300078 scopus 로고    scopus 로고
    • FIMO: Scanning for occurrences of a given motif
    • Grant CE, Bailey TL, Noble WS, (2011) FIMO: scanning for occurrences of a given motif. Bioinformatics 27: 1017-1018
    • (2011) Bioinformatics , vol.27 , pp. 1017-1018
    • Grant, C.E.1    Bailey, T.L.2    Noble, W.S.3
  • 24
    • 0020083498 scopus 로고
    • The meaning and use of the area under a receiver operating characteristic (ROC) curve
    • Hanley JA, McNeil BJ, (1982) The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143: 29-36 (Pubitemid 12142173)
    • (1982) Radiology , vol.143 , Issue.1 , pp. 29-36
    • Hanley, J.A.1    McNeil, B.J.2
  • 26
    • 70349636598 scopus 로고    scopus 로고
    • Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns
    • Kaleta C, de Figueiredo LF, Schuster S, (2009) Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns. Genome Res 19: 1872-1883
    • (2009) Genome Res , vol.19 , pp. 1872-1883
    • Kaleta, C.1    De Figueiredo, L.F.2    Schuster, S.3
  • 27
  • 28
    • 84866090747 scopus 로고    scopus 로고
    • Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks
    • Kelk SM, Olivier BG, Stougie L, Bruggeman FJ, (2012) Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks. Sci Rep 2: 580
    • (2012) Sci Rep , vol.2 , pp. 580
    • Kelk, S.M.1    Olivier, B.G.2    Stougie, L.3    Bruggeman, F.J.4
  • 29
    • 22844450110 scopus 로고    scopus 로고
    • Systematic interpretation of genetic interactions using protein networks
    • DOI 10.1038/nbt1096
    • Kelley R, Ideker T, (2005) Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 23: 561-566 (Pubitemid 41724894)
    • (2005) Nature Biotechnology , vol.23 , Issue.5 , pp. 561-566
    • Kelley, R.1    Ideker, T.2
  • 31
    • 84861123691 scopus 로고    scopus 로고
    • Ten years of pathway analysis: Current approaches and outstanding challenges
    • Khatri P, Sirota M, Butte AJ, (2012) Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol 8: e1002375
    • (2012) PLoS Comput Biol , vol.8
    • Khatri, P.1    Sirota, M.2    Butte, A.J.3
  • 33
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 36
    • 84858439602 scopus 로고    scopus 로고
    • Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
    • Lewis NE, Nagarajan H, Palsson BO, (2012) Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev 10: 291-305
    • (2012) Nat Rev , vol.10 , pp. 291-305
    • Lewis, N.E.1    Nagarajan, H.2    Palsson, B.O.3
  • 37
    • 77953514760 scopus 로고    scopus 로고
    • Which metabolic pathways generate and characterize the flux space? A comparison among elementary modes, extreme pathways and minimal generators
    • Llaneras F, Pico J, (2010) Which metabolic pathways generate and characterize the flux space? A comparison among elementary modes, extreme pathways and minimal generators. J Biomed Biotechnol 2010: 753904
    • (2010) J Biomed Biotechnol , vol.2010 , pp. 753904
    • Llaneras, F.1    Pico, J.2
  • 38
    • 65649126379 scopus 로고    scopus 로고
    • Connecting extracellular metabolomic measurements to intracellular flux states in yeast
    • Mo ML, Palsson BO, Herrgard MJ, (2009) Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst Biol 3: 37
    • (2009) BMC Syst Biol , vol.3 , pp. 37
    • Mo, M.L.1    Palsson, B.O.2    Herrgard, M.J.3
  • 40
    • 84865571240 scopus 로고    scopus 로고
    • Network context and selection in the evolution to enzyme specificity
    • (New York NY)
    • Nam H, Lewis NE, Lerman JA, Lee DH, Chang RL, Kim D, Palsson BO, (2012) Network context and selection in the evolution to enzyme specificity. Science (New York NY) 337: 1101-1104
    • (2012) Science , vol.337 , pp. 1101-1104
    • Nam, H.1    Lewis, N.E.2    Lerman, J.A.3    Lee, D.H.4    Chang, R.L.5    Kim, D.6    Palsson, B.O.7
  • 43
    • 77958460555 scopus 로고    scopus 로고
    • The challenges of integrating multi-omic datasets
    • Palsson B, Zengler K, (2010) The challenges of integrating multi-omic datasets. Nat Chem Biol 6: 787-789
    • (2010) Nat Chem Biol , vol.6 , pp. 787-789
    • Palsson, B.1    Zengler, K.2
  • 45
    • 83255164884 scopus 로고    scopus 로고
    • Comprehensive genome-wide protein-DNA interactions detected at single nucleotide resolution
    • Rhee HS, Pugh BF, (2011) Comprehensive genome-wide protein-DNA interactions detected at single nucleotide resolution. Cell 147: 1408-1419
    • (2011) Cell , vol.147 , pp. 1408-1419
    • Rhee, H.S.1    Pugh, B.F.2
  • 48
    • 0034615791 scopus 로고    scopus 로고
    • Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective
    • Schilling CH, Letscher D, Palsson BO, (2000) Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J Theor Biol 203: 229-248
    • (2000) J Theor Biol , vol.203 , pp. 229-248
    • Schilling, C.H.1    Letscher, D.2    Palsson, B.O.3
  • 49
    • 78751473491 scopus 로고    scopus 로고
    • Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli
    • Shimada T, Yamamoto K, Ishihama A, (2011) Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli. J Bacteriol 193: 649-659
    • (2011) J Bacteriol , vol.193 , pp. 649-659
    • Shimada, T.1    Yamamoto, K.2    Ishihama, A.3
  • 51
    • 0037079050 scopus 로고    scopus 로고
    • Metabolic network structure determines key aspects of functionality and regulation
    • DOI 10.1038/nature01166
    • 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 (Pubitemid 35340124)
    • (2002) Nature , vol.420 , Issue.6912 , pp. 190-193
    • Stelling, J.1    Klamt, S.2    Bettenbrock, K.3    Schuster, S.4    Gilles, E.D.5
  • 53
    • 0036237890 scopus 로고    scopus 로고
    • Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase system?
    • DOI 10.1128/JB.184.10.2603-2613.2002
    • Tramonti A, Visca P, De Canio M, Falconi M, De Biase D, (2002) Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase system. J Bacteriol 184: 2603-2613 (Pubitemid 34457026)
    • (2002) Journal of Bacteriology , vol.184 , Issue.10 , pp. 2603-2613
    • Tramonti, A.1    Visca, P.2    De Canio, M.3    Falconi, M.4    De Biase, D.5
  • 55
    • 79960610255 scopus 로고    scopus 로고
    • Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs
    • Wessely F, Bartl M, Guthke R, Li P, Schuster S, Kaleta C, (2011) Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Mol Syst Biol 7: 515
    • (2011) Mol Syst Biol , vol.7 , pp. 515
    • Wessely, F.1    Bartl, M.2    Guthke, R.3    Li, P.4    Schuster, S.5    Kaleta, C.6
  • 56
    • 0142092727 scopus 로고    scopus 로고
    • Reconstructing metabolic flux vectors from extreme pathways: Defining the α-spectrum
    • DOI 10.1016/S0022-5193(03)00168-1
    • Wiback SJ, Mahadevan R, Palsson BO, (2003) Decomposing steady state flux vectors into extreme pathways: defining the alpha-spectrum. J Theor Biol 224: 313-324 (Pubitemid 37297428)
    • (2003) Journal of Theoretical Biology , vol.224 , Issue.3 , pp. 313-324
    • Wiback, S.J.1    Mahadevan, R.2    Palsson, B.O.3
  • 57
    • 36348959154 scopus 로고    scopus 로고
    • Estimation of the number of extreme pathways for metabolic networks
    • Yeung M, Thiele I, Palsson BØ, (2007) Estimation of the number of extreme pathways for metabolic networks. BMC Bioinformatics 8: 363
    • (2007) BMC Bioinformatics , vol.8 , pp. 363
    • Yeung, M.1    Thiele, I.2    Palsson, BØ.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.