Hyperdigraph-theoretic analysis of the EGFR signaling network: Initial steps leading to GTP:Ras complex formation

Journal of Computational Biology

Volumn 11, Issue 5, 2004, Pages 812-842

  Oliveira, Joseph S ^a   Jones Oliveira, Janet B ^a   Dixon, David A ^b   Bailey, Colin G ^c   Gull, Dean W ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF ALABAMA   (United States)

^c VICTORIA UNIVERSITY OF WELLINGTON   (New Zealand)

Author keywords

Algebraic combinatorial model; Biochemical pathways; Cell signaling; Complex formation; Distributions; Epidermal growth factor receptor (EGFR); GTP:RAS; Hyperdigraphs; Invariants; Minimal circuits; Network; Petri nets; Pinch points

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; RAS PROTEIN;

ARTICLE; BIOINFORMATICS; COMPLEX FORMATION; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION;

COMPUTATIONAL BIOLOGY; GUANOSINE TRIPHOSPHATE; MODELS, BIOLOGICAL; RAS PROTEINS; RECEPTOR, EPIDERMAL GROWTH FACTOR; SIGNAL TRANSDUCTION;

EID: 8444219727     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2004.11.812     Document Type: Article

References (30)

1. Bachem, A., and Kern, W. 1991. Linear Programming Duality: An Introduction to Oriented Matroids, Springer-Verlag, New York, NY.
2. Bajzer, Z., Myers, A.C., and Vuk-Pavlovic, S. 1989. Binding, internalization, and intracellular processing of proteins interacting with recycling receptors-A kinetic analysis. J. Biol. Chem. 264, 13623-13631.
3. Bhalla, U.S., and Iyengar, R. 1999. Emergent properties of networks of biological signaling pathways. Science 283, 381-387.
4. Berge, C. 1973. Graphs and Hypergraphs, American Elsevier, New York, NY
5. Colom, J. M., and Silva, M. 1990. Convex geometry and semiflows in P/T nets: A comparative study of algorithms for computation of minimal P-semiflows. Lecture Notes in Computer Science 483, 79-112.
6. Diestel, R. 2000. Graph Theory, 2nd ed., Springer, New York, NY.
7. French, A.R., and Lauffenburger, D.A. 1997. Controlling receptor/ligand trafficking: Effects of cellular and molecular properties on endosomal sorting. Ann. Biomed. Eng. 25, 690-707.
8. Garey, M., and Johnson, D. 1979. Computers and Intractability: A Guide to the Theory of NP-Completeness, W.H. Freeman, San Francisco, CA.
9. Gex-Fabry, M., and De Lisi, C. 1984. Receptor-mediated endocytosis: A model and its implications for experimental analysis. Am. J. Physiol. 247, R768-R779.
10. Gibbons, A. 1985. Algorithmic Graph Theory, Cambridge University Press, New York, NY.
11. Haugh, J.M., and Lauffenburger, D.A. 1998. Analysis of receptor internalization as a mechanism for modulating signal transduction. J. Theor. Biol. 195, 187-218.
12. Ideker, T., Thorsson, V., Ranish, J.A., Christmas, R., Buhler, J., Eng, J.K., Bumgarner, R., Goodlett, D.R., Aebersold, R., and Hood, L. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934.
13. Jones, N.D., Landweber, L.H., and Lien, Y.E. 1977. Complexity of some problems in Petri-nets. Theor. Comput. Sci. 4, 277-299.
14. 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.
15. Lund, K.A., Opresko, L.K., Starbuck, C., Walsh, B.J., and Wiley, H.S. 1990. Quantitative analysis of the endocytic system involved in hormone-induced receptor internalization. J. Biol. Chem. 265, 15713-15723.
16. Narayanan, H. 1997. Submodular functions on electrical networks. Ann. Dis. Math., North-Holland, Elsevier, New York.
17. Oliveira, J.S., Bailey, G.G., Jones-Oliveira, J.B., and Dixon, D.A. 2001. An algebraic-combinatorial model for the identification and mapping of biochemical pathways. Bull. Math. Biol. 63, 1163-1196.
18. Oliveira, J.S., Bailey, G.G., Jones-Oliveira, J.B., Dixon, D.A., Gull, D.W., and Chandler, M.L. 2003. A computational model for the identification of biochemical pathways in the Krebs cycle. J. Comp. Biol. 10(1), 57-82.
19. Reddy, V.N., Liebman, M.N., and Mavrovouniotis, M.L. 1996. Qualitative analysis of biochemical reaction systems. Comp. Biol. Med. 26, 9-24.
20. Reisig, W. 1985. Petri Nets, An Introduction, Springer-Verlag, New York, NY.
21. Resat, B.H., Ewald, J.A., Dixon, D.A., and Wiley, H.S. 2003. An integrated model of EGF receptor trafficking and signal transduction. Biophys. J., accepted 2003.
22. Schuster, S., Dandekar, T., and Fell, D.A. 1999. Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering. TIBTECH 17, 53-60.
23. Schuster, S., Fell, D.A., and Dandekar, T. 2000. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nature Biotechnol. 18, 326-332.
24. Schuster, S., Hilgetag, C., Woods, J.H., and Fell, D.A. 2002a. Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism. J. Math. Biol. 45, 153-181.
25. Schuster, S., Pfeiffer, T., Moldenhauer, F., Koch, I., and Dandekar, T. 2002b. Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to mycoplasma pneumoniae. BioInformatics 18(2), 351-361.
26. Sipser, M. 1997. Introduction to the Theory of Computation, PWS Publishing, Boston, MA.
27. Starke, PH. 1998. Analyse von Petri-Netz-Modellen, Teubner, Stuttgart.
28. Szép, J., and Forgó, F. 1985. Introduction to the Theory of Games, Kluwer Academic, Boston, MA.
29. Sorkin, A., Waters, C., Overholser, K.A., and Carpenter, G. 1991. Multiple autophosphorylation site mutations of the epidermal growth-factor receptor-Analysis of kinase-activity and endocytosis. J. Biol Chem. 266, 8355-8362.
30. Wiley, H.S., and Cunningham, D.D. 1981. A steady-state model for analyzing the cellular-binding internalization and degradation of polypeptide ligands. Cell 25, 433-440.