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Volumn 84, Issue 2, 2006, Pages 153-174

Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks

Author keywords

Qualitative analysis; Sign algebra; Steady state shift; Systems biology

Indexed keywords

BIOLOGICAL PROCESSES; DNA; GRAPHICAL METHOD; METABOLISM;

EID: 33646010660     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2005.10.006     Document Type: Article
Times cited : (27)

References (55)
  • 1
    • 1242274449 scopus 로고    scopus 로고
    • Detection of multi-stability, bifurcations, and hysteresis in a large class of biological positive-feedback systems
    • Angeli J., Ferrell J.J., and Sontag E. Detection of multi-stability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. PNAS (2004) 1822-1827
    • (2004) PNAS , pp. 1822-1827
    • Angeli, J.1    Ferrell, J.J.2    Sontag, E.3
  • 2
    • 0031021873 scopus 로고    scopus 로고
    • Glycolysis in bloodstream from trypanasoma brucei can be understood in terms of the kinetics of the glycotic enzymes
    • Bakker B.M., Michels P.A.M., Opperdoes F.R., and Westerhoff H.V. Glycolysis in bloodstream from trypanasoma brucei can be understood in terms of the kinetics of the glycotic enzymes. J. Biol. Chem. 272 (1997) 3207-3215
    • (1997) J. Biol. Chem. , vol.272 , pp. 3207-3215
    • Bakker, B.M.1    Michels, P.A.M.2    Opperdoes, F.R.3    Westerhoff, H.V.4
  • 3
    • 85194583592 scopus 로고    scopus 로고
    • Batt, G., Ropers, D., de Jong, H., Geiselmann, J., Mateescu, R., Page, M., Schneider, D., 2005. Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in escherichia coli. Bioinformatics 21 (Suppl. 1), i19-i28, special issue ISMB-2005.
  • 4
    • 0042125048 scopus 로고    scopus 로고
    • Revising regulatory networks: from expression data to linear causal models
    • Bay S., Shrager J., Pohorille A., and Langley P. Revising regulatory networks: from expression data to linear causal models. J. Biomed. Inform. 35 (2003) 289-297
    • (2003) J. Biomed. Inform. , vol.35 , pp. 289-297
    • Bay, S.1    Shrager, J.2    Pohorille, A.3    Langley, P.4
  • 6
    • 2942516004 scopus 로고    scopus 로고
    • Ab initio reconstruction of metabolic pathways
    • Boyer F., and Viari A. Ab initio reconstruction of metabolic pathways. Bioinformatics 19 Suppl. 2 (2003)
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Boyer, F.1    Viari, A.2
  • 7
    • 0345618182 scopus 로고    scopus 로고
    • Combining inductive logic programming, active learning and robotics to discover the function of genes
    • Bryant C., Muggleton S., Olivier S., Kell D., Reiser P., and King R. Combining inductive logic programming, active learning and robotics to discover the function of genes. Electron. Trans. Artif. Intel. 5 (2001) 1-36
    • (2001) Electron. Trans. Artif. Intel. , vol.5 , pp. 1-36
    • Bryant, C.1    Muggleton, S.2    Olivier, S.3    Kell, D.4    Reiser, P.5    King, R.6
  • 8
    • 85194563855 scopus 로고    scopus 로고
    • Calvano, S., Xiao, W., Richards, D., Felciano, R., Baker, H., Cho, R., Chen, R., Brownstein, B., Cobb, J., Tschoeke, S., Miller-Graziano, C., Moldawer, L., Mindrinos, M., Davis, R., Tompkins, R., Lowry, S., IA, L. S. C. R. P., published online Augest 31, 2005. A network-based analysis of systemic inflammation in humans. Nature.
  • 9
    • 85194535565 scopus 로고    scopus 로고
    • Calzone, L., Chabrier-Rivier, N., Fages, F., Soliman, S., 2005. A machine learning approach to biochemical reaction rules discovery. In: Francis, J., Doyle III, (Eds.), Proceedings of Foundations of Systems Biology and Engineering FOSBE'05, Santa Barbara, pp. 375-379
  • 12
    • 35048889119 scopus 로고    scopus 로고
    • Qualitative modelling of genetic networks: from logical regulatory graphs to standard petri nets
    • Chaouiya C., Remy E., Ruet P., and Thieffry D. Qualitative modelling of genetic networks: from logical regulatory graphs to standard petri nets. Lect. Note Comput. Sci. 3099 (2004) 137-156
    • (2004) Lect. Note Comput. Sci. , vol.3099 , pp. 137-156
    • Chaouiya, C.1    Remy, E.2    Ruet, P.3    Thieffry, D.4
  • 13
    • 18844380444 scopus 로고    scopus 로고
    • Robustness and fragility of boolean models for genetic regulatory networks
    • Chaves M., Albert R., and Sontag E. Robustness and fragility of boolean models for genetic regulatory networks. J. Theor. Biol. 235 (2005) 431-449
    • (2005) J. Theor. Biol. , vol.235 , pp. 431-449
    • Chaves, M.1    Albert, R.2    Sontag, E.3
  • 14
    • 0001622226 scopus 로고
    • Toward a systematic determination of complex reaction mechanisms
    • Chevalier T., Schreiber T., and Ross J. Toward a systematic determination of complex reaction mechanisms. J. Phys. Chem. 97 (1993)
    • (1993) J. Phys. Chem. , vol.97
    • Chevalier, T.1    Schreiber, T.2    Ross, J.3
  • 15
  • 16
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: a literature review
    • de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J. Comp. Biol. 9 1 (2002) 69-105
    • (2002) J. Comp. Biol. , vol.9 , Issue.1 , pp. 69-105
    • de Jong, H.1
  • 18
    • 85194553994 scopus 로고    scopus 로고
    • Dormoy, J., 1988. Controlling qualitative resolution. In: Proceedings of the seventh National Conference on Artificial Intelligence, AAAI88', Saint-Paul, Minn.
  • 19
    • 0032489447 scopus 로고    scopus 로고
    • Propsects for antiparasitic drugs: the case of trypanasoma brucei, the causative agent of african sleeping sickness
    • Eisenthal R., and Cornish-Bowden A. Propsects for antiparasitic drugs: the case of trypanasoma brucei, the causative agent of african sleeping sickness. J. Biol. Chem 272 (1998) 5500-5505
    • (1998) J. Biol. Chem , vol.272 , pp. 5500-5505
    • Eisenthal, R.1    Cornish-Bowden, A.2
  • 21
    • 14344265954 scopus 로고    scopus 로고
    • Symbolic reachable set computation of piecewise affine hybrid automata and its application to biological modelling: delta-notch protein signalling
    • Ghoshn R., and Andomlin C. Symbolic reachable set computation of piecewise affine hybrid automata and its application to biological modelling: delta-notch protein signalling. Syst. Biol. 1 1 (2004) 170-183
    • (2004) Syst. Biol. , vol.1 , Issue.1 , pp. 170-183
    • Ghoshn, R.1    Andomlin, C.2
  • 23
    • 1542344471 scopus 로고    scopus 로고
    • Fatty acid regulation of gene transcription
    • Jump D. Fatty acid regulation of gene transcription. Crit. Rev. Clin. Lab. Sci. 41 1 (2004) 41-78
    • (2004) Crit. Rev. Clin. Lab. Sci. , vol.41 , Issue.1 , pp. 41-78
    • Jump, D.1
  • 24
    • 85194531771 scopus 로고    scopus 로고
    • Kaern, M., A. Elston, T., Blake, W. J., Collins, J.J., 2005. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6, 451-464.
  • 25
    • 0035984564 scopus 로고    scopus 로고
    • Practical approaches to analyzing results of microarray experiments
    • Kaminski N., and Friedman N. Practical approaches to analyzing results of microarray experiments. Am. J. Resp. Cell Mol. Biol. 27 (2002) 125-213
    • (2002) Am. J. Resp. Cell Mol. Biol. , vol.27 , pp. 125-213
    • Kaminski, N.1    Friedman, N.2
  • 28
    • 18744388601 scopus 로고    scopus 로고
    • On the use of qualitative reasoning to simulate and identify metabolic pathways
    • King R., Garrett S., and Coghill G. On the use of qualitative reasoning to simulate and identify metabolic pathways. Bioinformatics 21 9 (2005) 2017-2026
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 2017-2026
    • King, R.1    Garrett, S.2    Coghill, G.3
  • 30
    • 85194547525 scopus 로고    scopus 로고
    • Langley, P., Shiran, O., Shrager, J., Todorovski, L., Pohorille, A., 2005. Constructing explanatory process models from biological data and knowledge. Artif. Intell. Med., in press.
  • 31
    • 21644455156 scopus 로고    scopus 로고
    • Requirement of pparalpha in maintaining phospholipid and triacylglycerol homeostasis during energy deprivation
    • Lee S., Chan W., Lo C., Wan D., Tsang D., and Cheung W. Requirement of pparalpha in maintaining phospholipid and triacylglycerol homeostasis during energy deprivation. J. Lipid. Res. 45 11 (2004) 2025-2037
    • (2004) J. Lipid. Res. , vol.45 , Issue.11 , pp. 2025-2037
    • Lee, S.1    Chan, W.2    Lo, C.3    Wan, D.4    Tsang, D.5    Cheung, W.6
  • 32
    • 0037088683 scopus 로고    scopus 로고
    • Diminished hepatic response to fasting/refeeding and liver x receptor agonists in mice with selective deficiency of sterol regulatory element-binding protein-1c
    • Liang G., Yang J., Horton J., Hammer R., Goldstein J., and Brown M. Diminished hepatic response to fasting/refeeding and liver x receptor agonists in mice with selective deficiency of sterol regulatory element-binding protein-1c. J. Biol. Chem. 277 15 (2002) 9520-9528
    • (2002) J. Biol. Chem. , vol.277 , Issue.15 , pp. 9520-9528
    • Liang, G.1    Yang, J.2    Horton, J.3    Hammer, R.4    Goldstein, J.5    Brown, M.6
  • 33
    • 0033648431 scopus 로고    scopus 로고
    • Hybrid petri net representation of gene regulatory network
    • Matsuno H., Doi A., Nagasaki M., and Miyano S. Hybrid petri net representation of gene regulatory network. Pac. Symp. Biocomput. 5 (2000) 341-352
    • (2000) Pac. Symp. Biocomput. , vol.5 , pp. 341-352
    • Matsuno, H.1    Doi, A.2    Nagasaki, M.3    Miyano, S.4
  • 35
    • 0030921160 scopus 로고    scopus 로고
    • Biochemistry by numbers: simulation of biochemical pathways with gepasi 3
    • Mendes P. Biochemistry by numbers: simulation of biochemical pathways with gepasi 3. Trends Biochem. Sci. 22 (1997) 36-363
    • (1997) Trends Biochem. Sci. , vol.22 , pp. 36-363
    • Mendes, P.1
  • 36
    • 0029823995 scopus 로고    scopus 로고
    • Peroxisome proliferators induce mouse liver stearoyl-coa desaturase 1 gene expression
    • Miller C., and Ntambi J. Peroxisome proliferators induce mouse liver stearoyl-coa desaturase 1 gene expression. Proc. Natl. Acad. Sci. U.S.A. 93 18 (1996) 9443-9448
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , Issue.18 , pp. 9443-9448
    • Miller, C.1    Ntambi, J.2
  • 37
    • 14844307159 scopus 로고    scopus 로고
    • Inferring quantitative models of regulatory networks from expression data
    • Nachman I., Regev A., and Friedman N. Inferring quantitative models of regulatory networks from expression data. Bioinformatics 20 (2004) i248-i256
    • (2004) Bioinformatics , vol.20
    • Nachman, I.1    Regev, A.2    Friedman, N.3
  • 38
    • 0036039741 scopus 로고    scopus 로고
    • The e-box like sterol regulatory element mediates the suppression of human Delta-6 desaturase gene by highly unsaturated fatty acids
    • Nara T., He W., Tang C., and Clarke S. The e-box like sterol regulatory element mediates the suppression of human Delta-6 desaturase gene by highly unsaturated fatty acids. Biochem. Biophys. Res. Commun. 296 1 (2002) 111-117
    • (2002) Biochem. Biophys. Res. Commun. , vol.296 , Issue.1 , pp. 111-117
    • Nara, T.1    He, W.2    Tang, C.3    Clarke, S.4
  • 40
    • 85194553119 scopus 로고    scopus 로고
    • Radulescu, O., Lagarrigue, S., Siegel, A., Veber, P., Le Borgne, M., 2005. Topology and static response of interaction networks in molecular biology. J. R. Soc. Interface, in press.
  • 41
    • 0037078982 scopus 로고    scopus 로고
    • Control exploitation and tolerance of intracellular noise
    • Rao C., Wolf D., and Arkin A. Control exploitation and tolerance of intracellular noise. Nature 420 (2002) 231-237
    • (2002) Nature , vol.420 , pp. 231-237
    • Rao, C.1    Wolf, D.2    Arkin, A.3
  • 43
    • 0035928464 scopus 로고    scopus 로고
    • A logical analysis of the drosophila gap-gene system
    • Sanchez L., and Thieffry D. A logical analysis of the drosophila gap-gene system. J. Theor. Biol. 211 (2001) 115-141
    • (2001) J. Theor. Biol. , vol.211 , pp. 115-141
    • Sanchez, L.1    Thieffry, D.2
  • 45
    • 7744230024 scopus 로고    scopus 로고
    • Graphic requirements for multistationarity
    • Soulé C. Graphic requirements for multistationarity. Complexus 1 (2003) 123-133
    • (2003) Complexus , vol.1 , pp. 123-133
    • Soulé, C.1
  • 46
    • 0345461478 scopus 로고    scopus 로고
    • Putative metabolic effects of the liver x receptor (lxr)
    • Steffensen K., and Gustafsson J. Putative metabolic effects of the liver x receptor (lxr). Diabetes 53 Supp 1 (2004) 36-52
    • (2004) Diabetes , vol.53 , Issue.SUPPL. 1 , pp. 36-52
    • Steffensen, K.1    Gustafsson, J.2
  • 47
    • 0142010520 scopus 로고    scopus 로고
    • Regulation of human Delta-6 desaturase gene transcription: identification of a functional direct repeat-1 element
    • Tang C., Cho H., Nakamura M., and Clarke S. Regulation of human Delta-6 desaturase gene transcription: identification of a functional direct repeat-1 element. J Lipid Res 44 4 (2003) 686-695
    • (2003) J Lipid Res , vol.44 , Issue.4 , pp. 686-695
    • Tang, C.1    Cho, H.2    Nakamura, M.3    Clarke, S.4
  • 48
    • 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
  • 51
    • 18744415587 scopus 로고    scopus 로고
    • Travé-Massuyès L., and Dague P. (Eds), Hermes sciences
    • In: Travé-Massuyès L., and Dague P. (Eds). Modèles et Raisonnements Qualitatifs (2003), Hermes sciences
    • (2003) Modèles et Raisonnements Qualitatifs
  • 52
    • 0037376655 scopus 로고    scopus 로고
    • Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell
    • Tyson J.J., Chen C., and Novák B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15 (2003) 221-231
    • (2003) Curr. Opin. Cell Biol. , vol.15 , pp. 221-231
    • Tyson, J.J.1    Chen, C.2    Novák, B.3
  • 53
    • 85194539353 scopus 로고    scopus 로고
    • Veber, P., Le Borgne, M., Siegel, A., Lagarrigue, S., Radulescu, O., 2005. Complex qualitative models in biology: a new approach. In: European Conference on Complex Systems 2005. Paris.
  • 54
    • 19544389868 scopus 로고    scopus 로고
    • Protein network inference from multiple genomic data: a supervised approach
    • Yamanishi Y., Vert J.-P., and Kanehisa M. Protein network inference from multiple genomic data: a supervised approach. Bioinformatics 20 (2004) i363-i370
    • (2004) Bioinformatics , vol.20
    • Yamanishi, Y.1    Vert, J.-P.2    Kanehisa, M.3
  • 55
    • 85194586426 scopus 로고    scopus 로고
    • Zupan, B., Bratko, I., Demsar, J., Beck, J., Kuspa, A., Shaunlsky, G., 2001. Abductive inference of genetic networks. In: Proceedings of the Eighth Conference on AI in Medicine in Europe: Artificial Intelligence Medicine. Lecture Notes In Computer Science, vol. 2101. pp. 304 - 313.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.