Network modeling of signal transduction: Establishing the global view

BioEssays

Volumn 30, Issue 11-12, 2008, Pages 1110-1125

  Kestler, Hans A ^a,b   Wawra, Christian ^a   Kracher, Barbara ^b   Kühl, Michael ^b  

^a UNIVERSITY HOSPITAL ULM   (Germany)

^b UNIVERSITY OF ULM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

STAT1 PROTEIN; STRESS ACTIVATED PROTEIN KINASE; WNT PROTEIN;

ANALYTICAL PARAMETERS; APOPTOSIS; CELL COMPARTMENTALIZATION; CELL DIFFERENTIATION; CELL MIGRATION; CELL NUCLEUS; CELL POLARITY; CELL PROLIFERATION; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SYSTEM; CYTOLOGY; DATA BASE; DEVELOPMENTAL BIOLOGY; EXTRACELLULAR MATRIX; GENE EXPRESSION; INFORMATION SCIENCE; INTERNET; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; METHODOLOGY; MOLECULAR BIOLOGY; NEGATIVE FEEDBACK; PROTEIN BINDING; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN STABILITY; REVIEW; SECOND MESSENGER; SIGNAL TRANSDUCTION; STATISTICAL MODEL; T LYMPHOCYTE; TARGET CELL; TRANSCRIPTION INITIATION; ANIMAL; BIOLOGICAL MODEL; CAENORHABDITIS ELEGANS; COMPUTER SIMULATION; DROSOPHILA MELANOGASTER; GENE EXPRESSION REGULATION; HUMAN; MOUSE; SYSTEMS BIOLOGY; THEORETICAL MODEL;

ANIMALS; CAENORHABDITIS ELEGANS; COMPUTER SIMULATION; DROSOPHILA MELANOGASTER; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HUMANS; MAP KINASE SIGNALING SYSTEM; MICE; MODELS, BIOLOGICAL; MODELS, THEORETICAL; SIGNAL TRANSDUCTION; SOFTWARE; SYSTEMS BIOLOGY;

EID: 58149159905     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20834     Document Type: Review

References (107)

1. Muller P, Kuttenkeuler D, Gesellchen V, Zeidler MP, Boutros M. 2005. Identification of JAK/STAT signalling components by genome-wide RNA interference. Nature 436:871-875.
2. DasGupta R, Kaykas A, Moon RT, Perrimon N. 2005. Functional genomic analysis of the Wnt-wingless signaling pathway. Science 308:826-833.
3. Friedman A, Perrimon N. 2006. A functional RNAi screen for regulators of receptor tyrosine kinase and ERK signalling. Nature 444:230-234.
4. Wilkens A. 2002. The Evolution of Developmental Pathways. Sunderland, MA: Sinauer Associates.
5. Turing AM. 1952. The chemical basis of morphogenesis. Phil Trans Roy Soc Lond B 237:37-72.
6. Gierer A, Meinhardt H. 1972. A theory for biological pattern formation. Kybernetics 12:30-39.
7. Westerhoff HV, Palsson BO. 2004. The evolution of molecular biology into systems biology. Nature biotechnology 22:1249-1252.
8. Huang S. 2004. Back to the biology in systems biology: what can we learn from biomolecular networks? Briefings in functional genomics & proteomics 2:279-297.
9. O'Malley MA, Dupre J. 2005. Fundamental issues in systems biology. BioEssays: news and reviews in molecular, cellular and developmental biology 27:1270-1276.
10. Hunter T. 1997. Oncoprotein networks. Cell 88:333-346.
11. Gerhart J. 1999. 1998 Warkany lecture: signaling pathways in development. Teratology 60:226-239.
12. Attisano L, Wrana JL. 2002. Signal transduction by the TGF-beta superfamily. Science 296:1646-1647.
13. Gilbert SF. 2006. Developmental Biology. Sunderlund, MA: Sinauer Associates.
14. Nüsslein-Volhard C, Wieschaus E. 1980. Mutations afecting segment number and polarity in Drosophila. Nature 287:795-801.
15. Friedman A, Perrimon N. 2007. Genetic screening for signal transduction in the era of network biology. Cell 128:225-231.
16. Giehl K, Imamichi Y, Menke A. 2007. Smad4-independent TGF-beta signaling in tumor cell migration. Cells Tissues Organs 185:123-130.
17. Moustakas A, Heldin CH. 2005. Non-Smad TGF-beta signals. J Cell Sci 118:3573-3584.
18. Logan CY, Nusse R. 2004. The Wnt signaling pathway in development and disease. Annu Rev Cell Dev Biol 20:781-810.
19. Veeman MT, Axelrod JD, Moon RT. 2003. A second canon. Functions and mechanisms of beta-catenin-independent Wnt signaling. Dev Cell 5:367-377.
20. Yang L, Lin C, Liu ZR. 2006. P68 RNA helicase mediates PDGF-induced epithelial mesenchymal transition by displacing Axin from beta-catenin. Cell 127:139-155.
21. Bottcher RT, Niehrs C. 2005. Fibroblast growth factor signaling during early vertebrate development. Endocr Rev 26:63-77.
22. Neumann M, Naumann M. 2007. Beyond IkappaBs: alternative regulation of NF-kappaB activity. FASEB J 21:2642-2654.
23. Neves SR, Iyengar R. 2002. Modeling of signaling networks. Bioessays 24:1110-1117.
24. Bhalla US, Iyengar R. 2001. Robustness of the bistable behavior of a biological signaling feedback loop. Chaos 11:221-226.
25. Bhalla US, Ram PT, Iyengar R. 2002. MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297:1018-1023.
26. Jho EH, Zhang T, Domon C, Joo CK, Freund JN, Costantini F. 2002. Wnt/ beta-catenin/Tcf signaling induces the transcription of Axin2, a negative regulator of the signaling pathway. Mol Cell Biol 22:1172-1183.
27. Lustig B, Jerchow B, Sachs M, Weiler S, Pietsch T, Karsten U, et al. 2002. Negative feedback loop of Wnt signaling through upregulation of conductin/axin2 in colorectal and liver tumors. Mol Cell Biol 22:1184-1193.
28. Niida A, Hiroko T, Kasai M, Furukawa Y, Nakamura Y, Suzuki Y, et al. 2004. DKK1, a negative regulator of Wnt signaling, is a target of the beta-catenin/TCF pathway. Oncogene 23:8520-8526.
29. Minowada G, Jarvis LA, Chi CL, Neubuser A, Sun X, Hacohen N, et al. 1999. Vertebrate Sprouty genes are induced by FGF signaling and can cause chondrodysplasia when overexpressed. Development 126:4465-4475.
30. Eblaghie MC, Lunn JS, Dickinson RJ, Munsterberg AE, Sanz-Ezquerro JJ, Farrell ER, et al. 2003. Negative feedback regulation of FGF signaling levels by Pyst1/MKP3 in chick embryos. Curr Biol 13:1009-1018.
31. Dequéant ML, Glynn E, Gaudenz K, Wahl M, Chen J, Mushegian A, Pourquiec C. 2006. A complex oscillating network of signaling genes underlies the mouse segmentation clock. Science 314:1595-1598.
32. Wawra C, Kühl M, Kestler HA. 2007. Extended analyses of the Wnt/ beta-catenin pathway: Robustness and oscillatory behaviour. FEBS Lett 581:4043-4048.
33. Tu X, Joeng KS, Nakayama KI, Nakayama K, Rajagopal J, et al. 2007. Noncanonical Wnt Signaling through G Protein-Linked PKCdelta Activation Promotes Bone Formation. Dev Cell 12:113-127.
34. Bikkavilli RK, Feigin ME, Malbon CC. 2008. G alpha o mediates WNT-JNK signaling through dishevelled 1 and 3, RhoA family members, and MEKK 1 and 4 in mammalian cells. J Cell Sci 121:234-245.
35. Wu X, Tu X, Joeng KS, Hilton MJ, Williams DA, Long F. 2008. Rac1 activation controls nuclear localization of beta-catenin during canonical Wnt signaling. Cell 133:340-353.
36. Gan XQ, Wang JY, Xi Y, Wu ZL, Li YP, Li L. 2008. Nuclear Dvl, c-Jun, beta-catenin, and TCF form a complex leading to stabilization of beta-catenin-TCF interaction. J Cell Biol 180:1087-1100.
37. Kestler HA, Kühl M. 2008. From individual Wnt pathways towards a Wnt signalling network. Phil Trans R Soc B 363:1333-1347.
38. Ishikawa A, Kitajima S, Takahashi Y, Kokubo H, Kanno J, et al. 2004. Mouse Nkd1, a Wnt antagonist, exhibits oscillatory gene expression in the PSM under the control of Notch signaling. Mech Dev 121:1443-1453.
39. Rousset R, Mack JA, Wharton KA Jr, Axelrod JD, Cadigan KM, et al. 2001. Naked cuticle targets dishevelled to antagonize Wnt signal transduction. Genes Dev 15:658-671.
40. Axelrod JD, Matsuno K, Artavanis-Tsakonas S, Perrimon N. 1996. Interaction between Wingless and Notch signaling pathways mediated by dishevelled. Science 271:1826-1832.
41. Nishita M, Hashimoto MK, Ogata S, Laurent MN, Ueno N, et al. 2000. Interaction between Wnt and TGF-beta signalling pathways during formation of Spemann's organizer. Nature 403:781-785.
42. Novak A, Hsu SC, Leung-Hagesteijn C, Radeva G, Papkoff J, et al. 1998. Cell adhesion and the integrin-linked kinase regulate the LEF-1 and beta-catenin signaling pathways. Proc Natl Acad Sci USA 95:4374-4379.
43. Hino S, Tanji C, Nakayama KI, Kikuchi A. 2005. Phosphorylation of beta-catenin by cyclic AMP-dependent protein kinase stabilizes beta-catenin through inhibition of its ubiquitination. Mol Cell Biol 25: 9063-9072.
44. Buchanan FG, DuBois RN. 2006. Connecting COX-2 and Wnt in cancer. Cancer Cell 9:6-8.
45. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, et al. 2003. A protein interaction map of Drosophila melanogaster. Science 302: 1727-1736.
46. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, et al. 2004. A map of the interactome network of the metazoan C. elegans. Science 303:540-543.
47. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. 2005. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122:957-968.
48. Colland F, Jacq X, Trouplin V, Mougin C, Groizeleau C, et al. 2004. Functional proteomics mapping of a human signaling pathway. Genome Res 14:1324-1332.
49. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627.
50. Puig O, Caspary F, Rigaut G, Rutz B, Bouveret E, et al. 2001. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24:218-229.
51. Angers S, Thorpe CJ, Biechele TL, Goldenberg SJ, Zheng N, et al. 2006. The KLHL12-Cullin-3 ubiquitin ligase negatively regulates the Wnt-beta-catenin pathway by targeting Dishevelled for degradation. Nat Cell Biol 8:348-357.
52. Major MB, Camp ND, Berndt JD, Yi X, Goldenberg SJ, et al. 2007. Wilms tumor suppressor WTX negatively regulates WNT/beta-catenin signaling. Science 316:1043-1046.
53. Perrimon N, Mathey-Prevot B. 2007. Applications of High-THroughput RNA interference screens to problems in cell and developmental biology. Genetics 175:7-16.
54. Sonnichsen B, Koski LB, Walsh A, Marschall P, Neumann B, et al. 2005. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434:462-469.
55. Gilbert D, Fua H, Gu X, Orton R, Robinson S, et al. 2006. Computational methodologies for modelling, analysis and simulation of signalling netowrks. Briefings in Bioinformatics 7:339-353.
56. Heinrich R, Schuster S. 1996. The regulation of cellular systems. New York: Chapman & Hall.
57. Wolkenhauer O, Sreenath SN, Wellstead P, Ullah M, Cho KH. 2005. A systems- and signal-oriented appraoch to intracellular dynamics. Biochemical Society Transactions 33:507-515.
58. Barabasi AL, Oltvai ZN. 2004. Network biology: understanding the cell's functional organization. Nat Rev Genet 5:101-113.
59. Zhu X, Gerstein M, Snyder M. 2007. Getting connected: analysis and principles of biological networks. Genes Dev 21:1010-1024.
60. Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, et al. 2005. Formation of regulatory patterns during signal propagation in a mammalian cellular network. Science 309:1078-1083.
61. Clauset A, Moore C, Newman ME. 2008. Hierarchical structure and the prediction of missing links in networks. Nature 453:98-101.
62. Markowetz F, Spang R. 2007. Inferring cellular networks - a review. BMC Bioinformatics 8(Suppl 6):S5.
63. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D. 2002. Network Motifs: Simple Building Blocks of Complex Networks. Science 298:824-827.
64. Alon U. 2007. An introduction to systems biology: Design principles of biological circuits. London: Chapman & Hall/CRC.
65. Kholodenko BN. 2007. Untangling the signalling wires. Nature Cell Biology 9:247-249.
66. Santos SD, Verveer PJ, Bastiaens PI. 2007. Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate. Nat Cell Biol 9:324-330.
67. Stelling J, Sauer U, Szallasi Z, Doyle FJ, Doyle J. 2004. Robustness of cellular functions. Cell 118:675-685.
68. Kitano H. 2007. The Theory of biological robustness and its implication for cancer. Bringmann P, Butcher EC, Parry G, Weiss B, editors. Systems Biology Applications and Perspectives, 69-88, Berlin: Springer.
69. Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W. 2006. Rules for modeling signal-transduction systems. Sci STKE 2006:re6.
70. Heiner M, Koch I, Will J. 2004. Model validation of biological pathways using Petri nets-demonstrated for apoptosis. Biosystems 75:15-28.
71. Wilkinson DJ. 2006. Stochastic Modelling for Systems Biology. Boca Raton, FL: Chapman & Hall/CRC.
72. Szallasi Z, Stelling J, Periwal V. 2006. System Modeling in cellular biology. Cambridge, MA: MIT press.
73. Harel D. 1987. Statecharts: A visual formalism for complex systems. Science of Computer Programming 8:231-274.
74. Thomas R. 1973. Boolean formalization of genetic control circuits. J Theor Biol 42:563-585.
75. Saez-Rodriguez J, Simeoni L, Lindquist JA, Hemenway R, Bommhardt U, et al. 2007. A logical model provides insights into T cell receptor signaling. PLoS Comput Biol 3:e163.
76. Amonlirdviman K, Khare NA, Tree DR, Chen WS, Axelrod JD, Tomlin CJ. 2005. Mathematical modeling of planar cell polarity to understand domineering nonautonomy. Science 307:423-426.
77. Nakamura T, Mine N, Nakaguchi E, Mochizuki A, Yamamoto M, et al. 2006. Generation of robust left-right Asymmetry in the mouse embryo requires a self-enhancement and lateral inhibition system. Developmental Cell 11:495-504.
78. Goldbeter A, Pourquie O. 2008. Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways. J Theoretical Biol.
79. Rodriguez-Gonzalez JG, Santillan M, Fowler AC, Mackey MC. 2007. The segmentation clock in mice: interaction between the Wnt and Notch signalling pathways. Journal of theoretical biology 248:37-47.
80. Aldridge BB, Burke JM, Lauffenburger DA, Sorger PK. 2006. Physicochemical modelling of cell signalling pathways. Nat Cell Biol 8:1195-1203.
81. Gillespie D. 1976. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Computational Physics 22:403-434.
82. Gillespie DT. 2001. Approximate accelerated stochastic simulation of chemically reacting system. J Physical Chem 115:1716-1733.
83. Gibson M, Bruck J. 2000. Efficient exact stochastic simulation of chemically reacting systems. J of Physical Chemistry A 104:1876-1888.
84. Gillespie D. 1977. Exact stochastic simulation of coupled chemical reactions. J Physical Chem 81:2340-2361.
85. Shudo E, Yang J, Yoshimura A, Iwasa Y. 2007. Robustness of the signal transduction system of the mammalian JAK/STAT pathway and dimerization steps. J Theoretical Biol 246:1-9.
86. Hornberg JJ, Binder B, Bruggeman FJ, Schoeberl B, Heinrich R, Westerhoff HV. 2005. Control of MAPK signalling: from complexity to what really matters. Oncogene 24:5533-5542.
87. Uhrmacher A, Kuttler C. 2006. Multi-level modeling in systems biology by discrete event approaches. Information Technology 48:148-153.
88. Schlitt T, Brazma A. 2005. Modelling gene networks at different organisational levels. FEBS Letters 579:1859-1866.
89. Ingolia NT. 2004. Topology and robustness in the Drosophila segment polarity network. PLoS Biol 2:e123.
90. Chaves M, Albert R, Sontag ED. 2005. Robustness and fragility of Boolean models for genetic regulatory networks. J Theor Biol 235:431-449.
91. Albert R, Othmer HG. 2003. The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J Theoretical Biol 223:1-18.
92. von Dassow G, Meir E, Munro EM, Odell GM. 2000. The segment polarity network is a robust developmental module. Nature 406:188-192.
93. Tian T, Harding A, Inder K, Plowman S, Parton RG, Hancock JF. 2007. Plasma membrane nanoswitches generate high-fidelity Ras signal transduction. Nat Cell Biol 9:905-914.
94. Klipp E, Liebermeister W, Helbig A, Kowald A, Schaber J. 2007. Systems biology standards - the community speaks. Nat Biotechnol 25: 390-391.
95. Levesque MP, Benfey PN. 2004. Systems biology. Curr Biol 14:R179-180.
96. Swedlow JR, Lewis SE, Goldberg IG. 2006. Modelling data across labs, genomes, space and time. Nat Cell Biol 8:1190-1194.
97. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, et al. 2003. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524-531.
98. Wingreen N, Botstein D. 2006. Back to the future: education for systems-level biologists. Nature Reviews Molecular Cell Biology: A users guide:S60-S63.
99. Bialek W, Botstein D. 2004. Introductory science and mathematics education for 21st-Century biologists. Science 303:788-790.
100. Wallingford JB, Habas R. 2005. The developmental biology of Dishevelled: an enigmatic protein governing cell fate and cell polarity. Development 132:4421-4436.
101. Semenov MV, Habas R, Macdonald BT, He X. 2007. SnapShot: Noncanonical Wnt Signaling Pathways. Cell 131:1378.
102. Macdonald BT, Semenov MV, He X. 2007. SnapShot: Wnt/beta-catenin signaling. Cell 131:1204.
103. De Jong H. 2002. Modeling and simulation of genetic regulators systems: A literature review. Journal of Computational Biology 9:67-103.
104. Kauffman SA. 1969. Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 22:437-467.
105. Kauffman SA. 1993. Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press.
106. Martin S, Zhang Z, Martino A, Faulon JL. 2007. Boolean dynamics of genetic regulatory networks inferred from microarray time series data. Bioinformatics 23:866-874.
107. Helikar T, Konvalina J, Heidel J, Rogers JA. 2008. Emergent decision-making in biological signal transduction networks. Proc Natl Acad Sci USA 105:1913-1918.