Propagation of kinetic uncertainties through a canonical topology of the TLR4 signaling network in different regions of biochemical reaction space

Theoretical Biology and Medical Modelling

Volumn 7, Issue 1, 2010, Pages

  Gutiérrez, Jayson ^a   St Laurent, Georges ^a,b   Urcuqui Inchima, Silvio ^a  

^a UNIVERSIDAD DE ANTIOQUIA   (Colombia)

^b BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TOLL LIKE RECEPTOR 4;

ARTICLE; CHEMISTRY; KINETICS; SIGNAL TRANSDUCTION; UNCERTAINTY;

KINETICS; SIGNAL TRANSDUCTION; TOLL-LIKE RECEPTOR 4; UNCERTAINTY;

EID: 77949446554     PISSN: None     EISSN: 17424682     Source Type: Journal    
DOI: 10.1186/1742-4682-7-7     Document Type: Article

References (63)

1. Emergent Properties of Networks of Biological Signaling Pathways. US Bhalla R Iyengar, Science 1999 283 381 387 10.1126/science.283.5400.381 9888852 (Pubitemid 129501099)
2. Complexity in Biological Signaling Systems. G Weng US Bhalla R Iyengar, Science 1999 284 92 96 10.1126/science.284.5411.92 10102825 (Pubitemid 29282052)
3. Cell Signaling Dynamics in Time and Space. B Kholodenko, Nat Rev Mol Cell Biol 2006 281 29 19925 19938
4. The Complexity of Cell Signaling and the Need for a New Mechanics. WS Hlavacek JR Faeder, Science Signaling 2009 2 81 e46 10.1126/scisignal.281pe46 19638613
5. Topology of Biological Networks and Reliability of Information Processing. K Klemm S Bornholdt, PNAS 2005 102 51 18414 18419 10.1073/pnas.0509132102 16339314
6. Emergent Decision-Making in Biological Signal Transduction Networks. T Helikar J Konvalina J Heidel JA Rogers, PNAS 2008 105 6 1913 1918 10.1073/pnas.0705088105 18250321 (Pubitemid 351439439)
7. Robustness in Bacterial Chemotaxis. U Alon MG Surette N Barkai S Leibler, Nature 1999 397 6715 168 171 10.1038/16483 9923680 (Pubitemid 29050922)
8. The Segment Polarity Network is a Robust Developmental Module. G von Dassow E Meir EM Munro GM Odell, Nature 2000 406 188 192 10.1038/35018085 10910359 (Pubitemid 30469001)
9. Robustness, Flexibility, and the Role of Lateral Inhibition in the Neurogenic Network. E Meir G von Dassow E Munro GM Odel, Curr Biol 2002 12 778 786 10.1016/S0960-9822(02)00839-4 12015114 (Pubitemid 34514363)
10. Transitions in the Model of Epithelial Patterning. M Pribyl CB Muratov SY Shvartsman, Dev Dyn 2003 226 1 155 159 10.1002/dvdy.10218 12508238 (Pubitemid 36043474)
11. Sloppiness, Robustness, and Evolvability in Systems Biology. BC Daniels YJ Chen JP Sethna RN Gutenkunst CR Myers, Curr Opin Biotech 2008 19 1:7
12. Universally Sloppy Parameter Sensitivities in Systems Biology Models. RN Gutenkunst JJ Waterfall FP Casey KS Brown CR Myers JP Sethna, PLoS Comput Biol 2007 3 10 189 10.1371/journal.pcbi.0030189 (Pubitemid 350043403)
13. A Developmental Systems Perspective on Epistasis: Computational Exploration of Mutational Interactions in Model Developmental Regulatory Networks. J Gutiérrez, PLoS ONE 2009 4 9 6823 10.1371/journal.pone. 0006823 19738908
14. Control of MAPK Signaling: From Complexity to what Really Matters. JJ Hornberg B Binder FJ Bruggeman B Schoeberl, et al. Oncogene 2005 24 5533 5542 10.1038/sj.onc.1208817 16007170 (Pubitemid 43119348)
15. Mathematical Models of Protein Kinase Signal Transduction. R Heinrich BG Neel TA Rapoport, Molecular Cell 2002 9 957 970 10.1016/S1097-2765(02)00528-2 12049733 (Pubitemid 34626667)
16. Robustness of Cellular Functions. J Stelling U Sauer Z Szallasi FJI Doyle J Doyle, Cell 2004 118 6 675 685 10.1016/j.cell.2004.09.008 15369668 (Pubitemid 39221728)
17. Robustness Properties of Circadian Clock Architectures. J Stelling ED Gilles FJ Doyle, PNAS 2004 101 36 13210 13215 10.1073/pnas.0401463101 15340155 (Pubitemid 39209644)
18. Mathematical Identification of Critical Reactions in the Interlocked Feedback Model. H Kurata T Tanaka F Ohnishi, PLoS ONE 2007 2 10 1103 10.1371/journal.pone.0001103 17971866
19. Robustness Analysis of EGFR Signaling Network with a Multi-Objective Evolutionary Algorithm. X Zou M Liu Z Pan, BioSystems 2008 91 245 261 10.1016/j.biosystems.2007.10.001 18053637 (Pubitemid 350297575)
20. Input-Output Behavior of ErbB Signaling Pathways as Revealed by a Mass Action Model Trained against Dynamic Data. WW Chen B Schoeberl PJ Jasper M Niepel, et al. Mol Syst Biol 2009 5 239 19156131
21. Geometry and Topology of Parameter Space: Investigating Measures of Robustness in Regulatory Networks. M Chaves A Sengupta ED Sontag, J Math Biol 2008 18987858
22. Shape, Size and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks. A Dayarian M Chaves ED Sontag AM Sengupta, PLoS Comput Biol 2009 5 1 1000256 10.1371/journal.pcbi.1000256 19119410
23. A Methodology for Performing Global Uncertainty and Sensitivity Analysis in Systems Biology. S Marino IB Hogue CJ Ray DE Kirschner, J Theor Biol 2008 254 178 196 10.1016/j.jtbi.2008.04.011 18572196
24. Insights into the Behavior of Systems Biology Models from dynamic Sensitivity and Identifiability Analysis: A Case Study of an NF-kB Signaling. H Yue M Brown J Knowles H Wang, et al. Molecular BioSystems 2006 640 640 649 10.1039/b609442b (Pubitemid 44772307)
25. Experimental Design in Systems Biology, Based on Parameter Sensitivity Analysis Using a Monte Carlo Method: A Case Study for the TNFalpha-Mediated NF-kB Signal Transduction Pathway. KH Cho SY Shin W Kolch O Wolkenhauer, Simulation 2003 79 11-12 1 15
26. Dynamic Modelling and Analysis of Biochemical Networks: Mechanism-based Models and Model-based Experiments. NAW Van Riel, Briefings in Bioinformatics 2006 7 4 364 374 10.1093/bib/bbl040 17107967
27. Glocal Robustness Analysis and Model Discrimination for Circadian Oscillators. M Hafner H Koeppl M Hasler A Wagner, PLoS Comput Biol 2009 5 10 1000534 10.1371/journal.pcbi.1000534 19834597
28. Investigating Differential Dynamics of the MAPK Signaling Cascade Using a Multi-Parametric Global Sensitivity analysis. J Yoon TS Deisboeck, PLoS ONE 2009 4 2 4560 10.1371/journal.pone.0004560 19234599
29. A Mechanistic Study of Evolvability Using the Mitogen-Activated Protein Kinase Cascade. HF Nijhout AM Berg WT Gibson, Evol Devel 2003 5 3 281 294 10.1046/j.1525-142X.2003.03035.x (Pubitemid 36684612)
30. The Statistical Mechanics of Complex Signaling Networks: Nerve Growth Factor Signaling. KS Brown CC Hill GA Calero CR Myers KH Lee, et al. Phys Biol 2004 1 184 195 10.1088/1478-3967/1/3/006 16204838 (Pubitemid 44362296)
31. Coordinating TLR-Activated Signaling Pathways in Cells of the Immune System. A Banerjee S Gerondakis, Immunol Cell Biol 2007 85 420 424 10.1038/sj.icb.7100098 17637696 (Pubitemid 47367508)
32. LPS/TLR4 signal Transduction Network. YC Lu WC Yeh PS Ohashi, Cytokine 2008 42 145 151 10.1016/j.cyto.2008.01.006 18304834
33. Toll-like Receptor Signal Transduction. J Krishnan K Selvarajoo M Tsuchiya G Lee S Choi, Experimental and Molecular Medicine 2007 39 4 421 438 17934330 (Pubitemid 47443856)
34. A Comprehensive Map of the Toll-like Receptor Signaling Network. K Oda H Kitano, Mol Syst Biol 2006 2006.0015
35. The Roles of TLRs, RLRs and NLRs in Pathogen Recognition. T Kaway S Akira, Int Immunol 2009 21 4 317 337 10.1093/intimm/dxp017 19246554
36. Cooperation of Toll-like Receptor Signals in Innate Immune Defence. G Trinchieri A Sher, Nat Rev Immunol 2007 7 3 179 190 10.1038/nri2038 17318230 (Pubitemid 46310482)
37. Toll-like Receptor Signaling. A Shizuo K Takeda, Nat Rev Immunol 2004 4 7 499 511 10.1038/nri1391 15229469
38. Kinetic Insulation as an Effective Mechanism for Achieving Pathway Specificity in Intracellular Signaling Networks. M Behar HG Dohlman TC Elston, PNAS 2007 104 41 16146 16151 10.1073/pnas.0703894104 17913886
39. Receptor Downregulation and Desensitization Enhance the Information Processing Ability of Signaling Receptors. H Shankaran HS Wiley H Resat, BMC Syst Biol 2007 1 48 10.1186/1752-0509-1-48 17996096
40. Cell Surface Receptors for Signal Transduction and Ligand Transport: A Design Principles Study. H Shankaran H Resat HS Wiley, PLoS Comput Biol 2007 3 6 101 10.1371/journal.pcbi.0030101 17542642
41. Signals and Systems: Towards a Systems Biology of Signal Transduction. J Gunawardena, Proceedings of the IEEE 2008 96 8 1386 1397 10.1109/JPROC.2008. 925413
42. A Global Analysis of Cross-Talk in a Mammalian Cellular Signalling Network. M Natarajan KM Lin RC Hsueh PC Sternweis R Ranganathan, Nat Cell Biol 2006 8 6 571 580 10.1038/ncb1418 16699502 (Pubitemid 43827349)
43. Deciphering Signaling Outcomes from a System of Complex Networks. RC Hsueh M Natarajan I Fraser B Pond J Liu S Mumby, et al. Science Signaling 2009 2 71 a22 10.1126/scisignal.2000054 19454649
44. Informatio-Theoretic Sensitivity Analysis: A General Method for Credit Assigment in Complex Networks. N Lüdtke S Panzeri M Brown DS Broomhead J Knowles MA Montemurro DB Kell, J R Soc Interface 2008 5 223 235 10.1098/rsif.2007.1079 17594961
45. Toll-like Receptor Signaling. S Akira K Takeda, Nat Rev Immunol 2004 4 499 511 10.1038/nri1391 15229469
46. Discovering Differential Activation Machinery of the Toll-like Receptor 4 Signaling Pathways in MYD88 Knockouts. K Selvarajoo, FEBS Letters 2006 580 1457 1464 10.1016/j.febslet.2006.01.046 16458306
47. Signaling Flux Redistribution at Toll-like Receptor Pathway Junctions. K Selvarajoo Y Takada J Gohda M Helmy, et al. PLoS ONE 2008 3 10 3430 10.1371/journal.pone.0003430 18927610
48. A Simple Mathematical Model of Signaling Resulting from the Binding of Lipopolysaccharide with Toll-like Receptor 4 Demonstrates Inherent Precoditioning Behavior. B Riviere Y Ephsteyn D Swigon Y Vodovotz, Mathematical Biosciences 2009 217 19 26 10.1016/j.mbs.2008.10.002 18950647
49. Detailed Qualitative Dynamic Knowledge Representation Using BioNetGen Model of TLR-4 Signaling and Preconditioning. GC An JR Faeder, Mathematical Biosciences 2009 217 53 63 10.1016/j.mbs.2008.08.013 18835283
50. Autoregulatory Feedback Loops Terminating the NF-B Response. F Renner ML Schmitz, Trends in Biochemical Sciences 2009 34 3 128 135 10.1016/j.tibs.2008. 12.003 19233657
51. Achieving Stability of Lipopolysaccharide-Induced NF-B Activation. MW Covert TH Leung JE Gaston D Baltimore, Science 2005 309 1854 1857 10.1126/science.1112304 16166516
52. Functional Plasticity of Macrophages: Reversible Adaptation to Changing Microenvironments. RD Stout J Suttles, J Leukoc Biol 2004 76 3 509 513 10.1189/jlb.0504272 15218057
53. In silico Identification of the key Components and Steps in IFN- Induced JAK-STAT Signaling Pathway. Z Zi HC Cho MH Sung X Xia, et al. FEBS Letters 2005 579 1101 1108 10.1016/j.febslet.2005.01.009 15710397
54. Global Sensitivity Analysis of Cell Signaling Transduction Networks Based on Latin Hypercube Sampling Method. J Jia H Yue T Liu H Wang, Bioinformatics and Biomedical Engineering, IEEE Xplore 2007 434 437 full-text
55. Positive- and Negative-Feedback Regulations Coordinate the Dynamic Behavior of the Ras-Raf-MEK-ERK Signal Transduction Pathway. SY Shin O Rath SM Choo F Fee, et al. J Cell Sci 2009 122 425 435 10.1242/jcs.036319 19158341
56. Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions. CA Giurumescu PW Sternberg AR Asthagiri, PLoS Comput Biol 2009 5 4 1000354 10.1371/journal.pcbi.1000354 19360093
57. Stimulus Specificity of Gene Expression Programs Determined by Temporal Control of IKK Activity. LW Shannon D Barken A Hoffmann, Science 2005 309 1857 1861 10.1126/science.1113319 16166517
58. Cell-Signaling Dynamics in Time and Space. BN Kholodenko, Nat Rev Mol Cell Biology 2006 7 165 176 10.1038/nrm1838
59. Systems Biology. Less is More in Modeling Large Genetic Networks. S Bornholdt, Science 2005 310 5747 449 451 10.1126/science.1119959 16239464
60. Can Complex Cellular Processes be Governed by Simple Linear Rules? K Selvarajoo M Tomita M Tsuchiya, J Bioinf Comput Biol 2009 7 1 243 268 10.1142/S0219720009003947
61. An Approach to the Preliminary Analysis of Environmental Systems. G Hornberger R Spear, J Environ Manage 2005 12 7 18
62. Systematic Parameter Estimation of Wathershed Acidification Model. FJ Chang JW Delleur, Hydrol Processes 1992 6 29 44 10.1002/hyp.3360060104
63. 2Degassing and pH in a Stream-Aquifer System. J Choi SM Hulseapple MH Conklin JW Harvery, J Hydrol 1998 209 297 310 10.1016/S0022-1694(98)00093-6