메뉴 건너뛰기




Volumn 9, Issue 73, 2012, Pages 1824-1835

Dramatic reduction of dimensionality in large biochemical networks owing to strong pair correlations

Author keywords

Biological networks; Dimension reduction; Gram determinant; Pair correlations

Indexed keywords

COVARIANCE MATRIX; EIGENVALUES AND EIGENFUNCTIONS; GENES; NETWORK ARCHITECTURE; RATE CONSTANTS; REACTION KINETICS;

EID: 84865094962     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2011.0896     Document Type: Article
Times cited : (8)

References (34)
  • 1
    • 28844441230 scopus 로고    scopus 로고
    • A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis
    • doi:10.1126/science.1116598
    • Janes, K. A., Albeck, J. G., Gaudet, S., Sorger, P. K., Lauffenburger, D. A. & Yaffe, M. B. 2005 A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 310, 1646-1653. (doi:10.1126/science.1116598)
    • (2005) Science , vol.310 , pp. 1646-1653
    • Janes, K.A.1    Albeck, J.G.2    Gaudet, S.3    Sorger, P.K.4    Lauffenburger, D.A.5    Yaffe, M.B.6
  • 2
    • 49549116189 scopus 로고    scopus 로고
    • Quantitative phosphoproteomic analysis of signaling network dynamics
    • doi:10.1016/j.copbio.2008.06.006
    • White, F. M. 2008 Quantitative phosphoproteomic analysis of signaling network dynamics. Curr. Opin. Biotechnol. 19, 404-409. (doi:10.1016/j.copbio. 2008.06.006)
    • (2008) Curr. Opin. Biotechnol. , vol.19 , pp. 404-409
    • White, F.M.1
  • 3
    • 72149093283 scopus 로고    scopus 로고
    • A new approach for quantitative phosphoproteomic dissection of signaling pathways applied to T cell receptor activation
    • doi:10.1074/mcp.M800307-MCP200
    • Nguyen, V. et al. 2009 A new approach for quantitative phosphoproteomic dissection of signaling pathways applied to T cell receptor activation. Mol. Cell Proteomics 8, 2418-2431. (doi:10.1074/mcp.M800307-MCP200)
    • (2009) Mol. Cell Proteomics , vol.8 , pp. 2418-2431
    • Nguyen, V.1
  • 4
    • 33750351769 scopus 로고    scopus 로고
    • Data-driven modelling of signal-transduction networks
    • doi:10.1038/nrm2041
    • Janes, K. A. & Yaffe, M. B. 2006 Data-driven modelling of signal-transduction networks. Nat. Rev. Mol. Cell. Biol. 7, 820-828. (doi:10.1038/nrm2041)
    • (2006) Nat. Rev. Mol. Cell. Biol. , vol.7 , pp. 820-828
    • Janes, K.A.1    Yaffe, M.B.2
  • 5
    • 65349179556 scopus 로고    scopus 로고
    • Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin- induced signaling
    • doi:10.1371/journal.pcbi.1000340
    • Aldridge, B. B., Saez-Rodriguez, J., Muhlich, J. L., Sorger, P. K. & Lauffenburger, D. A. 2009 Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput. Biol. 5, e1000340. (doi:10.1371/journal.pcbi.1000340)
    • (2009) PLoS Comput. Biol. , vol.5
    • Aldridge, B.B.1    Saez-Rodriguez, J.2    Muhlich, J.L.3    Sorger, P.K.4    Lauffenburger, D.A.5
  • 6
    • 0000325341 scopus 로고
    • On lines and planes of closest fit to systems of points in space
    • Pearson, K. 1901 On lines and planes of closest fit to systems of points in space. Philos. Mag. 2, 559-572.
    • (1901) Philos. Mag. , vol.2 , pp. 559-572
    • Pearson, K.1
  • 7
    • 58149421595 scopus 로고
    • Analysis of a complex of statistical variables into principal components
    • doi:10.1037/h0070888
    • Hotelling, H. 1933 Analysis of a complex of statistical variables into principal components. J. Educ. Psychol. 24, 498-520. (doi:10.1037/h0070888)
    • (1933) J. Educ. Psychol. , vol.24 , pp. 498-520
    • Hotelling, H.1
  • 8
    • 27644496624 scopus 로고    scopus 로고
    • A compendium of signals and responses triggered by prodeath and prosurvival cytokines
    • doi:10.1074/mcp.M500158-MCP200
    • Gaudet, S., Janes, K. A., Albeck, J. G., Pace, E. A., Lauffenburger, D. A. & Sorger, P. K. 2005 A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol. Cell. Proteomics 4, 1569-1590. (doi:10.1074/mcp.M500158-MCP200)
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1569-1590
    • Gaudet, S.1    Janes, K.A.2    Albeck, J.G.3    Pace, E.A.4    Lauffenburger, D.A.5    Sorger, P.K.6
  • 9
    • 4544381664 scopus 로고    scopus 로고
    • Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data
    • doi:10.1089/1066527041887258
    • Janes, K. A., Kelly, J. R., Gaudet, S., Albeck, J. G., Sorger, P. K. & Lauffenburger, D. A. 2004 Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data. J. Comput. Biol. 11, 544-561. (doi:10.1089/1066527041887258)
    • (2004) J. Comput. Biol. , vol.11 , pp. 544-561
    • Janes, K.A.1    Kelly, J.R.2    Gaudet, S.3    Albeck, J.G.4    Sorger, P.K.5    Lauffenburger, D.A.6
  • 10
    • 53749085729 scopus 로고    scopus 로고
    • Cytokine-induced signaling networks prioritize dynamic range over signal strength
    • doi:10.1016/j.cell.2008.08.034
    • Janes, K. A., Reinhardt, H. C. & Yaffe, M. B. 2008 Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell 135, 343-354. (doi:10.1016/j.cell.2008.08.034)
    • (2008) Cell , vol.135 , pp. 343-354
    • Janes, K.A.1    Reinhardt, H.C.2    Yaffe, M.B.3
  • 11
    • 34547623194 scopus 로고    scopus 로고
    • Common effector processing mediates cell-specific responses to stimuli
    • doi:10.1038/nature06001
    • Miller-Jensen, K., Janes, K. A., Brugge, J. S. & Lauffenburger, D. A. 2007 Common effector processing mediates cell-specific responses to stimuli. Nature 448, 604-608. (doi:10.1038/nature06001)
    • (2007) Nature , vol.448 , pp. 604-608
    • Miller-Jensen, K.1    Janes, K.A.2    Brugge, J.S.3    Lauffenburger, D.A.4
  • 13
    • 0004270403 scopus 로고
    • 3rd edn. Oxford, UK: Pergamon Press
    • Landau, L. D. & Lifshits, E. M. 1976 Mechanics, vol. 1, 3rd edn. Oxford, UK: Pergamon Press.
    • (1976) Mechanics , vol.1
    • Landau, L.D.1    Lifshits, E.M.2
  • 14
    • 37649025842 scopus 로고    scopus 로고
    • A mathematical tool for exploring the dynamics of biological networks
    • doi:10.1073/pnas.0709955104
    • Barbano, P. E., Spivak, M., Flajolet, M., Nairn, A. C., Greengard, P. & Greengard, L. 2007 A mathematical tool for exploring the dynamics of biological networks. Proc. Natl Acad. Sci. USA 104, 19 169-19 174. (doi:10.1073/pnas.0709955104)
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 19169-19174
    • Barbano, P.E.1    Spivak, M.2    Flajolet, M.3    Nairn, A.C.4    Greengard, P.5    Greengard, L.6
  • 15
    • 52949144952 scopus 로고    scopus 로고
    • Top-down analysis of temporal hierarchy in biochemical reaction networks
    • doi:10.1371/journal.pcbi.1000177
    • Jamshidi, N. & Palsson, B. O. 2008 Top-down analysis of temporal hierarchy in biochemical reaction networks. PLoS Comput. Biol. 4, e1000177. (doi:10.1371/journal.pcbi.1000177)
    • (2008) PLoS Comput. Biol. , vol.4
    • Jamshidi, N.1    Palsson, B.O.2
  • 16
    • 50649101988 scopus 로고    scopus 로고
    • From the determination of complex reaction mechanisms to systems biology
    • doi:10.1146/annurev.biochem.77.102507.115132
    • Ross, J. 2008 From the determination of complex reaction mechanisms to systems biology. Annu. Rev. Biochem. 77, 479-494. (doi:10.1146/annurev.biochem. 77.102507.115132)
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 479-494
    • Ross, J.1
  • 19
    • 67650360968 scopus 로고    scopus 로고
    • Unlimited multistability in multisite phosphorylation systems
    • doi:10.1038/nature08102
    • Thomson, M. & Gunawardena, J. 2009 Unlimited multistability in multisite phosphorylation systems. Nature 460, 274-277. (doi:10.1038/ nature08102)
    • (2009) Nature , vol.460 , pp. 274-277
    • Thomson, M.1    Gunawardena, J.2
  • 21
    • 62049085839 scopus 로고    scopus 로고
    • Modern multivariate statistical techniques regression, classification, and manifold learning
    • New York, NY: Springer
    • Izenman, A. J. 2008 Modern multivariate statistical techniques regression, classification, and manifold learning. In Springer texts in statistics, vol. xxv. New York, NY: Springer.
    • (2008) Springer Texts in Statistics , vol.25
    • Izenman, A.J.1
  • 22
    • 0033570090 scopus 로고    scopus 로고
    • Quantification of short term signaling by the epidermal growth factor receptor
    • doi:10.1074/jbc.274.42.30169
    • Kholodenko, B. N., Demin, O. V., Moehren, G. & Hoek, J. B. 1999 Quantification of short term signaling by the epidermal growth factor receptor. J. Biol. Chem. 274, 30 169-30 181. (doi:10.1074/jbc.274.42.30169)
    • (1999) J. Biol. Chem. , vol.274 , pp. 30169-30181
    • Kholodenko, B.N.1    Demin, O.V.2    Moehren, G.3    Hoek, J.B.4
  • 23
    • 10244219918 scopus 로고    scopus 로고
    • BIONETGEN: Software for rule-based modeling of signal transduction based on the interactions of molecular domains
    • doi:10.1093/bioinformatics/bth378
    • Blinov, M. L., Faeder, J. R., Goldstein, B. & Hlavacek, W. S. 2004 BIONETGEN: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics 20, 3289-3291. (doi:10.1093/bioinformatics/bth378)
    • (2004) Bioinformatics , vol.20 , pp. 3289-3291
    • Blinov, M.L.1    Faeder, J.R.2    Goldstein, B.3    Hlavacek, W.S.4
  • 24
    • 32044469862 scopus 로고    scopus 로고
    • A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity
    • doi:10.1016/j.biosystems.2005.06.014
    • Blinov, M. L., Faeder, J. R., Goldstein, B. & Hlavacek, W. S. 2006 A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. Biosystems 83, 136-151. (doi:10.1016/j.biosystems.2005.06.014)
    • (2006) Biosystems , vol.83 , pp. 136-151
    • Blinov, M.L.1    Faeder, J.R.2    Goldstein, B.3    Hlavacek, W.S.4
  • 25
    • 72949108077 scopus 로고    scopus 로고
    • Pairing computation with experimentation: A powerful coupling for understanding T cell signalling
    • doi:10.1038/nri2688
    • Chakraborty, A. K. & Das, J. 2010 Pairing computation with experimentation: a powerful coupling for understanding T cell signalling. Nat. Rev. Immunol. 10, 59-71. (doi:10.1038/nri2688)
    • (2010) Nat. Rev. Immunol. , vol.10 , pp. 59-71
    • Chakraborty, A.K.1    Das, J.2
  • 26
    • 58249092059 scopus 로고    scopus 로고
    • Digital signaling and hysteresis characterize Ras activation in lymphoid cells
    • doi:10.1016/j.cell.2008.11.051
    • Das, J., Ho, M., Zikherman, J., Govern, C., Yang, M., Weiss, A., Chakraborty, A. K. & Roose, J. P. 2009 Digital signaling and hysteresis characterize Ras activation in lymphoid cells. Cell 136, 337-351. (doi:10.1016/j.cell.2008.11.051)
    • (2009) Cell , vol.136 , pp. 337-351
    • Das, J.1    Ho, M.2    Zikherman, J.3    Govern, C.4    Yang, M.5    Weiss, A.6    Chakraborty, A.K.7    Roose, J.P.8
  • 27
    • 0036532226 scopus 로고    scopus 로고
    • Self-perpetuating states in signal transduction: Positive feedback, double-negative feedback and bistability
    • doi:10.1016/s0955-0674(02)00314-9
    • Ferrell Jr, J. E. 2002 Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr. Opin. Cell Biol. 14, 140-148. (doi:10.1016/s0955-0674(02)00314-9)
    • (2002) Curr. Opin. Cell Biol. , vol.14 , pp. 140-148
    • Ferrell Jr., J.E.1
  • 29
    • 0037044575 scopus 로고    scopus 로고
    • The IκB-NF-κB signaling module: Temporal control and selective gene activation
    • doi:10.1126/science.1071914
    • Hoffmann, A., Levchenko, A., Scott, M. L. & Baltimore, D. 2002 The IκB-NF-κB signaling module: temporal control and selective gene activation. Science 298, 1241-1245. (doi:10.1126/science.1071914)
    • (2002) Science , vol.298 , pp. 1241-1245
    • Hoffmann, A.1    Levchenko, A.2    Scott, M.L.3    Baltimore, D.4
  • 30
    • 7444254365 scopus 로고    scopus 로고
    • Oscillations in NF-κB signaling control the dynamics of gene expression
    • doi:10.1126/science.1099962
    • Nelson, D. E. et al. 2004 Oscillations in NF-κB signaling control the dynamics of gene expression. Science 306, 704-708. (doi:10.1126/science. 1099962)
    • (2004) Science , vol.306 , pp. 704-708
    • Nelson, D.E.1
  • 31
    • 34249857117 scopus 로고    scopus 로고
    • Oscillation patterns in negative loops
    • doi:10.1073/pnas.0610759104
    • Pigolotti, S., Krishna, S. & Jensen, M. H. 2007 Oscillation patterns in negative loops. Proc. Natl Acad. Sci. USA 104, 6533-6537. (doi:10.1073/pnas.0610759104)
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 6533-6537
    • Pigolotti, S.1    Krishna, S.2    Jensen, M.H.3
  • 33
    • 0034704222 scopus 로고    scopus 로고
    • Nonlinear dimensionality reduction by locally linear embedding
    • doi:10.1126/science.290.5500.2323
    • Roweis, S. T. & Saul, L. K. 2000 Nonlinear dimensionality reduction by locally linear embedding. Science 290, 2323-2326. (doi:10.1126/science.290. 5500.2323)
    • (2000) Science , vol.290 , pp. 2323-2326
    • Roweis, S.T.1    Saul, L.K.2
  • 34
    • 77949289122 scopus 로고    scopus 로고
    • Clusters from higher order correlations
    • doi:10.1016/j.physleta.2010.02.021
    • Schulman, L. S. 2010 Clusters from higher order correlations. Phys. Lett. A 374, 1625-1630. (doi:10.1016/j.physleta.2010.02.021)
    • (2010) Phys. Lett. A , vol.374 , pp. 1625-1630
    • Schulman, L.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.