Sensitivity, principal component and flux analysis applied to signal transduction: The case of epidermal growth factor mediated signaling

Bioinformatics

Volumn 21, Issue 7, 2005, Pages 1194-1202

  Liu, Gang ^a   Swihart, Mark T ^a   Neelamegham, Sriram ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR; EPIDERMAL GROWTH FACTOR RECEPTOR; MITOGEN ACTIVATED PROTEIN KINASE; PROTEIN SHC;

ARTICLE; ARTIFICIAL NEURAL NETWORK; BIOASSAY; BIOINFORMATICS; CHEMICAL REACTION; CONCENTRATION RESPONSE; CONTROLLED STUDY; GENOMICS; HIGH THROUGHPUT SCREENING; INFORMATION PROCESSING; MATHEMATICAL MODEL; NONHUMAN; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEIN TRANSPORT; PROTEOMICS; QUANTITATIVE ANALYSIS; RECEPTOR BINDING; SENSITIVITY ANALYSIS; SIGNAL TRANSDUCTION;

EID: 16344394782     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti118     Document Type: Article

References (33)

1. Alter,O., Brown,P.O. and Botstein,D. (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl Acad. Sci. USA, 97, 10101-10106.
2. Batzer,A.G., Blaikie,P., Nelson,K., Schlessinger,J. and Margolis, B. (1995) The phosphotyrosine interaction domain of Shc binds an LXNPXY motif on the epidermal growth factor receptor. Mol. Cell Biol., 15, 4403-4409.
3. Bhalla,U.S. and Iyengar,R. (1999) Emergent properties of networks of biological signaling pathways. Science, 283, 381-387.
4. Chi-ying,F. and Ferrell,J.E.J. (1996) Ultrasensivity in the mitogen-activated protein kinase cascade. Proc. Natl Acad. Sci. USA 93, 10078-10083.
5. Edwards,J.S., Ibarra,R.U. and Palsson,B.O. (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol., 19, 125-130.
6. Fell,D. (1997) Metabolic control analysis. In Understanding the Control of Metabolism. Portland Press, London, pp. 101-132.
7. Fussenegger,M., Bailey,J.E. and Varner,J. (2000) A mathematical model of caspase function in apoptosis. Nat. Biotechnol. 18, 768-774.
8. Gardner,T.S., di Bernardo,D., Lorenz,D. and Collins,J.J. (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science, 301, 102-105.
9. Gong,Y. and Zhao,X. (2003) Shc-dependent pathway is redundant but dominant in MAPK cascade activation by EGF receptors: a modeling inference. FEBS Lett., 554, 467-472.
10. Heinrich,R., Neel,B.G. and Rapoport,T.A. (2002) Mathematical models of protein kinase signal transduction. Mol. Cell, 9, 957-970.
11. Heinrich,R. and Rapoport,T.A. (1974) A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem., 42, 89-95.
12. Holter,N.S., Mitra,M., Maritan,A., Cieplak,M., Banavar,J.R. and Fedoroff,N.V. (2000) Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc. Natl Acad. Sci. USA, 97, 8409-8414.
13. Kacser,H. and Burns,J.A. (1973) The control of flux. Symp. Soc. Exp. Biol., 27, 65-104.
14. Kauffman,K.J., Pajerowski,J.D., Jamshidi,N., Palsson,B.O. and Edwards,J.S. (2002) Description and analysis of metabolic connectivity and dynamics in the human red blood cell. Biophys. J., 83, 646-662.
15. Kholodenko,B.N., Demin,O.V., Moehren,G. and Hoek,J.B. (1999) Quantification of short term signaling by the epidermal growth factor receptor. J. Biol. Chem., 274, 30169-30181.
16. Kholodenko,B.N., Kiyatkin,A., Bruggeman,F.J., Sontag,E., Westerhoff,H.V. and Hoek,J.B. (2002) Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc. Natl Acad. Sci. USA, 99, 12841-12846.
17. Kikuchi,S., Tominaga,D., Arita,M., Takahashi,K. and Tomita,M. (2003) Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics, 19, 643-650.
18. Kuharsky,A.L. and Fogelson,A.L. (2001) Surface-mediated control of blood coagulation: the role of binding site densities and platelet deposition. Biophys. J., 80, 1050-1074.
19. Lee,K.H., Dinner,A.R., Tu,C., Campi,G., Raychaudhuri,S., Varma,R., Sims,T.N., Burack,W.R., Wu,H., Warg,J. et al. (2003) The immunological synapse balances T cell receptor signaling and degradation. Science, 302, 1218-1222.
20. Morrison,D.K. and Cutler,R.E. (1997) The complexity of Raf-1 regulation. Curr. Opin. Cell Biol., 9, 174-179.
21. Rapoport,T.A., Otto,M. and Heinrich,R. (1977) An extended model of the glycolysis in erythrocytes. Acta. Biol. Med. Ger., 36, 461-468.
22. Resat,H., Ewald,J.A., Dixon,D.A. and Wiley,H.S. (2003) An integrated model of epidermal growth factor receptor trafficking and signal transduction. Biophys. J., 85, 730-743.
23. Sachs,K., Gifford,D., Jaakkola,T., Sorger,P. and Lauffenburger,D.A. (2002) Bayesian network approach to cell signaling pathway modeling. Sci. STKE, 2002, PE38.
24. Sasaoka,T., Langlois,W.J., Leitner,J.W., Draznin,B. and Olefsky,J.M. (1994) The signaling pathway coupling epidermal growth factor receptors to activation of p21 ras. J. Biol. Chem., 269 32621-32625.
25. Sastry,L., Lin,W., Wong,W.T., Di Fiore,P.P., Scoppa,C.A. and King,C.R. (1995) Quantitative analysis of Grb2-Sos1 interaction: the N-terminal SH3 domain of Grb2 mediates affinity. Oncogene, 11 1107-1112.
26. Savageau,M.A. (1976) Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology. Addison-Wesley, Reading, MA.
27. Schoeberl,B., Eichler-Jonsson,C., Gilles,E.D. and Muller,G. (2002) Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat. Biotechnol. 20, 370-375.
28. Starbuck,C. and Lauffenburger,D.A. (1992) Mathematical model for the effects of epidermal growth factor receptor trafficking dynamics on fibroblast proliferation responses. Biotechnol. Prog., 8, 132-143.
29. Stephanopoulos,G.N., Aristidou,A.A. and Nielsen,J. (1998) Metabloic flux analysis. In Metabolic Engineering, Principles and Methodologies. Academic Press, New York, pp. 313-350.
30. Tomita,M., Hashimoto,K., Takahashi,K., Shimizu,T.S., Matsuzaki,Y., Miyoshi,F., Saito,K., Tarida,S., Yugi,K., Venter,J.C. and Hutchison,3rd, C.A. (1999) E-CELL: software environment for whole-cell simulation. Bioinformatics, 15, 72-84.
31. Varma,A., Morbidelli,M. and Wu,H. (1999) Parametric Sensitivity in Chemical Systems. Cambridge University Press, New York.
32. Vaseghi,S., Baumeister,A., Rizzi,M. and Reuss,M. (1999) In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae. Metab. Eng., 1, 128-140.
33. Vieira,A.V, Lamaze,C. and Schmid,S.L. (1996) Control of EGF receptor signaling by clathrin-mediated endocytosis. Science, 274, 2086-2089.