Inference of signaling and gene regulatory networks by steady-state perturbation experiments: Structure and accuracy

Journal of Theoretical Biology

Volumn 232, Issue 3, 2005, Pages 427-441

  Andrec, Michael ^a,b,e   Kholodenko, Boris N ^c   Levy, Ronald M ^a,b   Sontag, Eduardo ^b,d  

^a State University of New Jersey   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c THOMAS JEFFERSON UNIVERSITY   (United States)

^d RUTGERS UNIVERSITY   (United States)

^e RUTGERS UNIVERSITY   (United States)

Author keywords

Black box; Module; Reverse engineering; Systems biology; Unravelling

Indexed keywords

MITOGEN ACTIVATED PROTEIN KINASE;

BIOLOGICAL PROCESSES; CELLS AND CELL COMPONENTS;

ACCURACY; ANALYTICAL ERROR; ARTICLE; DATA ANALYSIS; EXCITATION; GENE CONTROL; GENE STRUCTURE; GEOMETRY; INHIBITION KINETICS; MATHEMATICAL COMPUTING; MOLECULAR INTERACTION; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; SIGNAL TRANSDUCTION; STEADY STATE; STRUCTURE ANALYSIS; TECHNIQUE;

ALGORITHMS; ANIMALS; CELL PHYSIOLOGY; GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 9644284380     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jtbi.2004.08.022     Document Type: Article

References (41)

1. M.D. Brand Top down metabolic control analysis J. Theor. Biol. 182 1996 351 360
2. P. Brazhnik, A. de la Fuente, and P. Mendes Gene networks how to put the function into genomics Trends Biotech. 20 2002 467 472
3. A.H. Brivanlou, and J.E.J. Darnell Signal transduction and the control of gene expression Science 295 2002 813 818
4. F. Canters, and H. Decleir The World in Perspective A Directory of World Map Projections 1989 Wiley Chichester
5. L. Chang, and M. Karin Mammalian MAP kinase signalling cascades Nature 410 2001 37 40
6. H. de Jong Modeling and simulation of genetic regulatory systems a literature review J. Comput. Biol. 9 2002 67 103
7. A. de la Fuente, P. Brazhnik, and P. Mendes Linking the genes inferring quantitative gene networks from microarray data Trends Genet. 18 2002 395 398
8. 2 approximation problems Linear Algebra Appl. 188-189 1993 163 205
9. J.J. Dongarra, J.R. Bunch, C.B. Moler, and G.W. Stewart LINPACK Users' Guide 1979 SIAM Press Philadelphia
10. G. Durando, and G. Mana Propagation of error analysis in a total least-squares estimator in absolute gravimetry Metrologia 39 2002 489 494
11. G. Eckart, and G. Young The approximation of one matrix by another of lower rank Psychometrica 1 1936 211 218
12. E.C. Fieller The distribution of the index in a normal bivariate population Biometrika 24 1932 428 440
13. N.I. Fisher, T. Lewis, and B.J.J. Embleton Statistical Analysis of Spherical Data 1987 Cambridge University Press Cambridge
14. T.S. Gardner, D. di Bernardo, D. Lorenz, and J.J. Collins Inferring genetic networks and identifying compound mode of action via expression profiling Science 301 2003 102 105
15. G.A. Gerhold Least-squares adjustment of weighted data to a general linear equation Am. J. Phys. 37 1969 156 161
16. G.H. Golub, and C.F. van Loan An analysis of the total least squares problem SIAM J. Numer. Anal. 17 1980 883 893
17. G.H. Golub, and C.F. van Loan Matrix Computations 1989 The Johns Hopkins University Press Baltimore
18. L.H. Hartwell, J.J. Hopfield, S. Leibler, and A.W. Murray From molecular to modular cell biology Nature 402 1999 C47 C52
19. J. Hasty, D. McMillen, F. Isaacs, and J.J. Collins Computational studies of gene regulatory networks in numero molecular biology Nat. Rev. Genet. 2 2001 268 279
20. C.A. Hazzalin, and L.C. Mahadevan MAPK-regulated transcription a continuously variable gene switch? Nat. Rev. Mol. Cell Biol. 3 2002 30 40
21. C.F. Huang, and J.E.J. Ferrell Ultrasensitivity in the mitogen-activated protein kinase cascade Proc. Natl Acad. Sci. USA 93 1996 10078 10083
22. B.N. Kholodenko Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades Eur. J. Biochem. 267 2000 1583 1588
23. Kholodenko, B.N., Sontag, E.D., 2002. Determination of functional network structure from local parameter dependence data. arXiv:physics/0205003.
24. B.N. Kholodenko, J.B. Hoek, H.V. Westerhoff, and G.C. Brown Quantification of information transfer via cellular signal transduction FEBS Lett. 414 1997 430 434
25. B.N. Kholodenko, O.V. Demin, G. Moehren, and J.B. Hoek Quantification of short term signaling by the epidermal growth factor receptor J. Biol. Chem. 274 1999 30169 30181
26. B.N. Kholodenko, A. Kiyatkin, F.J. Bruggeman, E. Sontag, H.V. Westerhoff, and J.B. Hoek Untangling the wires a strategy to trace functional interactions in signaling and gene networks Proc. Natl Acad. Sci. USA 99 2002 12841 12846
27. D.A. Lauffenburger Cell signaling pathways as control modules complexity for simplicity? Proc. Natl Acad. Sci. USA 97 2000 5031 5033
28. M. Lefebvre, R.K. Keeler, R. Sobie, and J. White Propagation of errors for matrix inversion Nucl. Insrum. Methods Phys. Res. A 451 2000 520 528
29. G. Marsaglia Ratios of normal variables and ratios of sums of uniform variables J. Am. Stat. Assoc. 60 1965 193 204
30. G. Moehren, N. Markevich, O. Demin, A. Kiyatkin, I. Goryanin, J.B. Hoek, and B.N. Kholodenko Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model Biochemistry 41 2002 306 320
31. Premoli, A., Rastello, M.L., 2002. The parametric quadratic form method for solving TLS problems with elementwise weighting. In: van Huffel, S., Lemmerling, P. (Eds.), Total Least Squares and Errors-in-Variables Modeling. Kluwer Academic Publishers, Dordrecht, pp. 67-76.
32. W.H. Press, S.A. Teukolsky, W.T. Vetterling, and B.P. Flannery Numerical Recipes in C The Art of Scientific Computing 1992 Cambridge University Press Cambridge
33. M. Ronen, R. Rosenberg, B.I. Shraiman, and U. Alon Assigning numbers to the arrows parametrizing a gene regulation network by using accurate expression kinetics Proc. Natl Acad. Sci. USA 99 2002 10555 10560
34. S.Y. Shvartsman, M.P. Hagan, A. Yacoub, P. Dent, H.S. Wiley, and D.A. Lauffenburger Autocrine loops with positive feedback enable context-dependent cell signaling Am. J. Physiol. 282 2002 C545 C559
35. P. Smolen, D.A. Baxter, and J.H. Byrne Frequency selectivity, multistability, and oscillations emerge from models of genetic regulatory systems Am. J. Physiol. 274 1998 C531 C542
36. J. Stark, R. Callard, and M. Hubank From the top down towards a predictive biology of signalling networks Trends Biotech. 21 2003 290 293
37. J.J. Tyson, K. Chen, and B. Novak Network dynamics and cell physiology Nat. Rev. Mol. Cell. Biol. 2 2001 908 916
38. S. van Huffel, and J. Vandewalle The Total Least Squares Problem Computational Aspects and Analysis 1991 SIAM Philadelphia
39. G. von Dassow, E. Meir, E.M. Munro, and G.M. Odell The segment polarity network is a robust developmental module Nature 406 2000 188 192
40. C. Widmann, S. Gibson, M.B. Jarpe, and G.L. Johnson Mitogen-activated protein kinase conservation of a three-kinase module from yeast to human Physiol. Rev. 79 1999 143 180
41. S. Wolfram Mathematica A System for Doing Mathematics by Computer 1991 Addison-Wesley Reading, MA