메뉴 건너뛰기




Volumn 7, Issue 4, 2007, Pages 215-234

Deterministic and stochastic models of NFκB pathway

Author keywords

Immune response; Mathematical modeling; NF B; Single cell; Stochastic regulation; Stochastic robustness; Systems biology

Indexed keywords

I KAPPA B KINASE ALPHA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; TUMOR NECROSIS FACTOR ALPHA;

EID: 36949039934     PISSN: 15307905     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12012-007-9003-x     Document Type: Review
Times cited : (22)

References (61)
  • 1
    • 33645429016 scopus 로고
    • Exact stochastic simulations of coupled chemical reactions
    • Gillespie, D. T. (1977). Exact stochastic simulations of coupled chemical reactions. The Journal of Physical Chemistry, 81, 2340-2361.
    • (1977) The Journal of Physical Chemistry , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 2
    • 0037109565 scopus 로고    scopus 로고
    • Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
    • Haseltine, E. L., & Rawlings, J. B. (2002). Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. The Journal of Chemical Physics, 117, 6959-6969.
    • (2002) The Journal of Chemical Physics , vol.117 , pp. 6959-6969
    • Haseltine, E.L.1    Rawlings, J.B.2
  • 3
    • 33847112418 scopus 로고    scopus 로고
    • The NF-κB regulatory networks
    • Brasier, A. R. (2006). The NF-κB regulatory networks. Cardiovascular Toxicology, 6, 111-130.
    • (2006) Cardiovascular Toxicology , vol.6 , pp. 111-130
    • Brasier, A.R.1
  • 4
    • 33645312379 scopus 로고    scopus 로고
    • Circuitry of nuclear κB factor signaling
    • Hoffmann, A., & Baltimore, D. (2006). Circuitry of nuclear κB factor signaling. Immunological Review, 210, 171-186.
    • (2006) Immunological Review , vol.210 , pp. 171-186
    • Hoffmann, A.1    Baltimore, D.2
  • 5
    • 0027168447 scopus 로고
    • NF-κB controls expression of inhibitor IκBα: Evidence for an inducible autoregulatory pathway
    • Sun, S.-C., Ganchi, P. A., Ballard, D. W., & Greene, W. C. (1993). NF-κB controls expression of inhibitor IκBα: Evidence for an inducible autoregulatory pathway. Science, 259, 1912-1915.
    • (1993) Science , vol.259 , pp. 1912-1915
    • Sun, S.-C.1    Ganchi, P.A.2    Ballard, D.W.3    Greene, W.C.4
  • 6
    • 0026699666 scopus 로고
    • Transcriptional activation of the tumor necrosis factor alpha-inducible zinc finger protein, A20, is mediated by kappa B elements
    • Krikos, A., Laherty, C. D., & Dixit, V. M. (1992). Transcriptional activation of the tumor necrosis factor alpha-inducible zinc finger protein, A20, is mediated by kappa B elements. The Journal of Biological Chemistry, 267, 17971-17976.
    • (1992) The Journal of Biological Chemistry , vol.267 , pp. 17971-17976
    • Krikos, A.1    Laherty, C.D.2    Dixit, V.M.3
  • 7
    • 0034730713 scopus 로고    scopus 로고
    • Failure to regulate TNF-induced NF-κB and cell death responses in A20-deficient mice
    • Lee, E. G., Boone, D. L., Chai, S., Libby, S. L., Chien, M., Lodolce, J. P., & Ma, A. (2000). Failure to regulate TNF-induced NF-κB and cell death responses in A20-deficient mice. Science, 289, 2350-2354.
    • (2000) Science , vol.289 , pp. 2350-2354
    • Lee, E.G.1    Boone, D.L.2    Chai, S.3    Libby, S.L.4    Chien, M.5    Lodolce, J.P.6    Ma, A.7
  • 8
    • 33645315510 scopus 로고    scopus 로고
    • Charting protein complexes, signaling pathways, and networks in the immune system
    • Bauch, A., & Superti-Furga, G. (2006). Charting protein complexes, signaling pathways, and networks in the immune system. Immunological Reviews, 210, 187-207.
    • (2006) Immunological Reviews , vol.210 , pp. 187-207
    • Bauch, A.1    Superti-Furga, G.2
  • 9
    • 0033600604 scopus 로고    scopus 로고
    • The beginning of the end: IκB kinase (IKK) and NF-κB activation
    • Karin, M. (1999). The beginning of the end: IκB kinase (IKK) and NF-κB activation. The Journal of Biological Chemistry, 274, 27339-27342.
    • (1999) The Journal of Biological Chemistry , vol.274 , pp. 27339-27342
    • Karin, M.1
  • 10
    • 0037044575 scopus 로고    scopus 로고
    • The IκB - NF - κB signaling module: Temporal control and selective gene activation
    • 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.
    • (2002) Science , vol.298 , pp. 1241-1245
    • Hoffmann, A.1    Levchenko, A.2    Scott, M.L.3    Baltimore, D.4
  • 11
    • 33747388013 scopus 로고    scopus 로고
    • IκBε provides negative feedback to control NF-κB oscillations, signaling dynamics, and inflammatory gene expression
    • DOI: 10.1083/jcb.200510155 JCB
    • Kearns, J. D., Basak, S., Werner, Sh. L., Huang, Ch. H., & Hoffmann, A. (2006). IκBε provides negative feedback to control NF-κB oscillations, signaling dynamics, and inflammatory gene expression. The Journal of Cell Biology DOI: 10.1083/jcb.200510155 JCB
    • (2006) The Journal of Cell Biology
    • Kearns, J.D.1    Basak, S.2    Werner, S.L.3    Huang, C.H.4    Hoffmann, A.5
  • 13
    • 31444432847 scopus 로고    scopus 로고
    • The influence of the signal dynamics of activated form of IKK on NFκB and anti-apoptotic gene expression: A systems biology approach
    • Park, S. G., Lee, T., Kang, H. Y., Park, K., Cho, K-H., & Jung, G. (2006). The influence of the signal dynamics of activated form of IKK on NFκB and anti-apoptotic gene expression: A systems biology approach. FEBS Letters, 580, 822-830.
    • (2006) FEBS Letters , vol.580 , pp. 822-830
    • Park, S.G.1    Lee, T.2    Kang, H.Y.3    Park, K.4    Cho, K.-H.5    Jung, G.6
  • 14
    • 0026075591 scopus 로고
    • Stochastic model for gene induction
    • Ko, M. S. H. (1991). Stochastic model for gene induction. Journal of Theoretical Biology, 153, 181-194.
    • (1991) Journal of Theoretical Biology , vol.153 , pp. 181-194
    • Ko, M.S.H.1
  • 16
    • 0035896577 scopus 로고    scopus 로고
    • The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression
    • Kierzek, A. M., Zaim, J., & Zielenkiewicz, P. (2001). The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression. The Journal of Biological Chemistry, 276, 8165-8172.
    • (2001) The Journal of Biological Chemistry , vol.276 , pp. 8165-8172
    • Kierzek, A.M.1    Zaim, J.2    Zielenkiewicz, P.3
  • 19
    • 19544379881 scopus 로고    scopus 로고
    • Stochasticity in gene expression from theories to phenotypes
    • Kærn, M., Elston, T. C., Blake, W. J., & Collins, J. J. (2005). Stochasticity in gene expression from theories to phenotypes. Nature Reviews, 6, 451-464.
    • (2005) Nature Reviews , vol.6 , pp. 451-464
    • Kærn, M.1    Elston, T.C.2    Blake, W.J.3    Collins, J.J.4
  • 21
  • 22
    • 0031738601 scopus 로고    scopus 로고
    • Dynamic changes in prolactin promoter activation in individual living lactotrophic cells
    • Takasuka, N., White, M. R. H., Wood, C. D., Robertson, W. R., & Davis, J. R. E. (1998). Dynamic changes in prolactin promoter activation in individual living lactotrophic cells. Endocrinology, 139, 1361-1368.
    • (1998) Endocrinology , vol.139 , pp. 1361-1368
    • Takasuka, N.1    White, M.R.H.2    Wood, C.D.3    Robertson, W.R.4    Davis, J.R.E.5
  • 24
    • 2942718723 scopus 로고    scopus 로고
    • Control of stochasticity in eukaryotic gene expression
    • Raser, J. M., & O'Shea, E. K. (2004). Control of stochasticity in eukaryotic gene expression. Science, 304, 1811-1814.
    • (2004) Science , vol.304 , pp. 1811-1814
    • Raser, J.M.1    O'Shea, E.K.2
  • 25
    • 0037119587 scopus 로고    scopus 로고
    • Stochastic gene expression in a single cell
    • Elowitz, M. B., Levine, A. J., Siggia, E. D., & Swain, P. S. (2002). Stochastic gene expression in a single cell. Science, 297, 1183-1186.
    • (2002) Science , vol.297 , pp. 1183-1186
    • Elowitz, M.B.1    Levine, A.J.2    Siggia, E.D.3    Swain, P.S.4
  • 26
    • 0035193294 scopus 로고    scopus 로고
    • Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations
    • Kepler, T. B., & Elston, T. C. (2001). Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations. Biophysical Journal, 81, 3116-3136.
    • (2001) Biophysical Journal , vol.81 , pp. 3116-3136
    • Kepler, T.B.1    Elston, T.C.2
  • 27
    • 0345708060 scopus 로고    scopus 로고
    • Fluctuations in transcription factor binding can be explain the graded and binary responses observed in inducible gene expression
    • Pirone, J. R., & Elston, T. C. (2004). Fluctuations in transcription factor binding can be explain the graded and binary responses observed in inducible gene expression. Journal of Theoretical Biology, 226, 111-121.
    • (2004) Journal of Theoretical Biology , vol.226 , pp. 111-121
    • Pirone, J.R.1    Elston, T.C.2
  • 30
    • 22944477377 scopus 로고    scopus 로고
    • The numerical stability of leaping methods for stochastic simulation of chemically reacting systems
    • Cao, Y., Petzold, L. R., Rathinam, M., Gillespie, D. T. (2004). The numerical stability of leaping methods for stochastic simulation of chemically reacting systems. The Journal of Chemical Physics, 121, 12169-12178.
    • (2004) The Journal of Chemical Physics , vol.121 , pp. 12169-12178
    • Cao, Y.1    Petzold, L.R.2    Rathinam, M.3    Gillespie, D.T.4
  • 31
    • 0035933994 scopus 로고    scopus 로고
    • Approximate accelerated stochastic simulation of chemically reacting system
    • Gillespie, D. T. (2001). Approximate accelerated stochastic simulation of chemically reacting system. The Journal of Physical Chemistry, 115, 1716-1733.
    • (2001) The Journal of Physical Chemistry , vol.115 , pp. 1716-1733
    • Gillespie, D.T.1
  • 32
    • 0037444724 scopus 로고    scopus 로고
    • Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
    • Rao, Ch. V., Arkin, A. P. (2003). Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm. The Journal of Chemical Physics, 118, 4999-5010.
    • (2003) The Journal of Chemical Physics , vol.118 , pp. 4999-5010
    • Rao, C.V.1    Arkin, A.P.2
  • 34
    • 1542345686 scopus 로고    scopus 로고
    • Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks
    • Puchalka, J., & Kierzek, A. M., (2004). Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks. Biophysical Journal, 86, 1357-1372.
    • (2004) Biophysical Journal , vol.86 , pp. 1357-1372
    • Puchalka, J.1    Kierzek, A.M.2
  • 37
    • 0037087597 scopus 로고    scopus 로고
    • Multi-parameter analysis of the kinetics of NF-κB signalling and transcription in single living cells
    • Nelson, G., Paraoan, L., Spiller, D. G., Wilde, G. J. C., Browne, A. M., & Djali, P. K., et al. (2002). Multi-parameter analysis of the kinetics of NF-κB signalling and transcription in single living cells. Journal of Cell Science, 115, 1137-1148.
    • (2002) Journal of Cell Science , vol.115 , pp. 1137-1148
    • Nelson, G.1    Paraoan, L.2    Spiller, D.G.3    Wilde, G.J.C.4    Browne, A.M.5    Djali, P.K.6
  • 39
    • 0037440199 scopus 로고    scopus 로고
    • Regulation of nuclear translocation of nuclear factor-κB RelA: Evidence for complex dynamics at the single-cell level
    • Schooley, K., Zhu, P., Dower, S. K., & Qwarnstrom, E. E. (2003). Regulation of nuclear translocation of nuclear factor-κB RelA: Evidence for complex dynamics at the single-cell level. The Biochemical Journal, 369, 331-339.
    • (2003) The Biochemical Journal , vol.369 , pp. 331-339
    • Schooley, K.1    Zhu, P.2    Dower, S.K.3    Qwarnstrom, E.E.4
  • 40
    • 0000718866 scopus 로고    scopus 로고
    • Modeling large biological systems from functional genomic data: Parameter estimation
    • H. Kitano Ed, MIT Press
    • Mendes, P. (2001). Modeling large biological systems from functional genomic data: Parameter estimation. In H. Kitano (Ed.), Foundations of systems biology (pp. 163-181). MIT Press.
    • (2001) Foundations of systems biology , pp. 163-181
    • Mendes, P.1
  • 41
    • 0027370376 scopus 로고
    • GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems
    • Mendes, P. (1993). GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems. Computer Applications in the Biosciences, 9, 563-571;
    • (1993) Computer Applications in the Biosciences , vol.9 , pp. 563-571
    • Mendes, P.1
  • 42
    • 0030921160 scopus 로고    scopus 로고
    • Biochemistry by numbers: Simulation of biochemical pathways with Gepasi 3
    • Mendes, P. (1997). Biochemistry by numbers: Simulation of biochemical pathways with Gepasi 3. Trends in Biochemical Sciences, 22, 361-363;
    • (1997) Trends in Biochemical Sciences , vol.22 , pp. 361-363
    • Mendes, P.1
  • 43
    • 0032406131 scopus 로고    scopus 로고
    • Nonlinear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation
    • Mendes, P., & Kell, D. B. (1998). Nonlinear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation. Bioinformatics, 14, 869-883.
    • (1998) Bioinformatics , vol.14 , pp. 869-883
    • Mendes, P.1    Kell, D.B.2
  • 45
    • 24944489952 scopus 로고    scopus 로고
    • Stimulus specificity of gene expression programs determined by temporal control of IKK activity
    • Werner, Sh. L., Barken, D., Hoffmann, A. (2005). Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science, 309, 1857-1861.
    • (2005) Science , vol.309 , pp. 1857-1861
    • Werner, S.L.1    Barken, D.2    Hoffmann, A.3
  • 46
    • 24944586285 scopus 로고    scopus 로고
    • Achieving stability of lipopolysaccharide-induced NFκB activation
    • Covert, M. W., Leung, Th. H., Gaston, J. E., & Baltimore, D. (2005). Achieving stability of lipopolysaccharide-induced NFκB activation. Science, 309, 1854-1857.
    • (2005) Science , vol.309 , pp. 1854-1857
    • Covert, M.W.1    Leung, T.H.2    Gaston, J.E.3    Baltimore, D.4
  • 47
    • 33646382406 scopus 로고    scopus 로고
    • Transient IκB kinase activity mediates temporal NFκB dynamics in response to wide rage of tumor necrosis factor-α doses
    • Cheong, R., Bergmann, A., Werner, Sh. L., Regal, J., Hoffmann, A., & Levchenko, A. (2006). Transient IκB kinase activity mediates temporal NFκB dynamics in response to wide rage of tumor necrosis factor-α doses. The Journal of Biological Chemistry, 281, 2945-2950.
    • (2006) The Journal of Biological Chemistry , vol.281 , pp. 2945-2950
    • Cheong, R.1    Bergmann, A.2    Werner, S.L.3    Regal, J.4    Hoffmann, A.5    Levchenko, A.6
  • 48
    • 0033596123 scopus 로고    scopus 로고
    • Genetic approaches in mice to understand Rel/NF-κB and IκB function: Transgenics and knockouts
    • Gerondakis, S., Grossmann, M., Nakamura, Y., Pohl, T., & Grumont, R. (1999). Genetic approaches in mice to understand Rel/NF-κB and IκB function: Transgenics and knockouts. Oncogene, 18, 6888-6895.
    • (1999) Oncogene , vol.18 , pp. 6888-6895
    • Gerondakis, S.1    Grossmann, M.2    Nakamura, Y.3    Pohl, T.4    Grumont, R.5
  • 49
    • 0037428385 scopus 로고    scopus 로고
    • The NF-κB activation in lymphotoxin receptor signaling depends on the phosphorylation of p65 at serine 536
    • Jiang, X., Takahashi, N., Matsui, N., Tetsuka, T., & Okamoto, T (2003). The NF-κB activation in lymphotoxin receptor signaling depends on the phosphorylation of p65 at serine 536. The Journal of Biological Chemistry, 278, 919-926.
    • (2003) The Journal of Biological Chemistry , vol.278 , pp. 919-926
    • Jiang, X.1    Takahashi, N.2    Matsui, N.3    Tetsuka, T.4    Okamoto, T.5
  • 50
    • 0242574987 scopus 로고    scopus 로고
    • Investigations into the analysis and modeling of the TNFα-mediated NFκB-signaling pathway
    • Cho, K.-H., Shin, S.-Y., Lee, H.-W., & Wolkenhauer, O. (2003). Investigations into the analysis and modeling of the TNFα-mediated NFκB-signaling pathway. Genome Research, 13, 2413-2422.
    • (2003) Genome Research , vol.13 , pp. 2413-2422
    • Cho, K.-H.1    Shin, S.-Y.2    Lee, H.-W.3    Wolkenhauer, O.4
  • 51
    • 0033537719 scopus 로고    scopus 로고
    • Positive and negative regulation of IκB kinase activity through IKKβ subunit phosphorylation
    • Delhase, M., Hayakawa, M., Chen, Y., & Karin, M. (1999). Positive and negative regulation of IκB kinase activity through IKKβ subunit phosphorylation. Science, 284, 309-313.
    • (1999) Science , vol.284 , pp. 309-313
    • Delhase, M.1    Hayakawa, M.2    Chen, Y.3    Karin, M.4
  • 53
    • 20444478655 scopus 로고    scopus 로고
    • Identification of direct genomic targets downstream of the NF-kappa B transcription factor mediating TNFα signaling
    • Tian, B., Nowak, D. E., Jamaluddin, M., Wang, S., & Brasier, A. R. (2005). Identification of direct genomic targets downstream of the NF-kappa B transcription factor mediating TNFα signaling. The Journal of Biological Chemistry, 280, 17435-17448.
    • (2005) The Journal of Biological Chemistry , vol.280 , pp. 17435-17448
    • Tian, B.1    Nowak, D.E.2    Jamaluddin, M.3    Wang, S.4    Brasier, A.R.5
  • 55
    • 0032562720 scopus 로고    scopus 로고
    • Visualization of single RNA transcripts in situ
    • Femino, A. M, Fay, F. S., Fogarty, K., & Singer, R. H. (1998). Visualization of single RNA transcripts in situ. Science, 280, 585-590.
    • (1998) Science , vol.280 , pp. 585-590
    • Femino, A.M.1    Fay, F.S.2    Fogarty, K.3    Singer, R.H.4
  • 56
    • 0034731365 scopus 로고    scopus 로고
    • Dynamic shuttling of nuclear factor kappa B between the nucleus and cytoplasm as a consequence of inhibitor dissociation
    • Carlotti, F, Dower, S. K., & Qwarnstrom, E. E. (2000). Dynamic shuttling of nuclear factor kappa B between the nucleus and cytoplasm as a consequence of inhibitor dissociation. The Journal of biological chemistry, 275, 41028-41034.
    • (2000) The Journal of biological chemistry , vol.275 , pp. 41028-41034
    • Carlotti, F.1    Dower, S.K.2    Qwarnstrom, E.E.3
  • 58
    • 15944426727 scopus 로고    scopus 로고
    • Comment on "Oscillations in NF-κB signaling control the dynamics of gene expression
    • Barken, D., Wang, Ch. J., Kearns, J., Cheong, R., Hoffmann, A., & Levchenko, A. (2005). Comment on "Oscillations in NF-κB signaling control the dynamics of gene expression". Science, 308, 52a.
    • (2005) Science , vol.308
    • Barken, D.1    Wang, C.J.2    Kearns, J.3    Cheong, R.4    Hoffmann, A.5    Levchenko, A.6
  • 60
    • 34249289745 scopus 로고    scopus 로고
    • TNF-α-induced NF-κB/Rel A Ser (276) phosphorylation and enhance some formation on the IL-8 promoter is mediated by an ROS-dependent PKAc pathway
    • Jamaluddin, M., Wang, S., Boldogh, I., Tian, B., & Brasier, A. R. (2007). TNF-α-induced NF-κB/Rel A Ser (276) phosphorylation and enhance some formation on the IL-8 promoter is mediated by an ROS-dependent PKAc pathway. Cellular Signalling, 19, 1419-1433.
    • (2007) Cellular Signalling , vol.19 , pp. 1419-1433
    • Jamaluddin, M.1    Wang, S.2    Boldogh, I.3    Tian, B.4    Brasier, A.R.5
  • 61
    • 26444435364 scopus 로고    scopus 로고
    • A TNF induced gene expression program under oscillatory NF-κB control
    • Tian, B., Nowak, D., & Brasier, A. R. (2005). A TNF induced gene expression program under oscillatory NF-κB control. BMC Genomics, 6, 137.
    • (2005) BMC Genomics , vol.6 , pp. 137
    • Tian, B.1    Nowak, D.2    Brasier, A.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.