Paradoxical results in perturbation-based signaling network reconstruction

Biophysical Journal

Volumn 106, Issue 12, 2014, Pages 2720-2728

  Prabakaran, Sudhakaran ^a   Gunawardena, Jeremy ^a   Sontag, Eduardo ^b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOGEN ACTIVATED PROTEIN KINASE; PHOSPHOPEPTIDE;

AMINO ACID SEQUENCE; ANIMAL; BIOLOGICAL MODEL; CHEMISTRY; HUMAN; MASS SPECTROMETRY; METABOLISM; MOLECULAR GENETICS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; XENOPUS;

AMINO ACID SEQUENCE; ANIMALS; HUMANS; MAP KINASE SIGNALING SYSTEM; MASS SPECTROMETRY; MITOGEN-ACTIVATED PROTEIN KINASES; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; PHOSPHOPEPTIDES; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; XENOPUS;

EID: 84902968947     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2014.04.031     Document Type: Article

References (47)

1. D.A. Lauffenburger Cell signaling pathways as control modules: complexity for simplicity? Proc. Natl. Acad. Sci. USA 97 2000 5031 5033 (Pubitemid 30313665)
2. L.H. Hartwell, and J.J. Hopfield A.W. Murray From molecular to modular cell biology Nature 402 1999 C47 C52
3. U.S. Bhalla, and R. Iyengar Functional modules in biological signaling networks Novartis Found. Symp. 239 2001 4 13 discussion 13-15., 45-51 (Pubitemid 33599031)
4. B.B. Aldridge, and J.M. Burke P.K. Sorger Physicochemical modeling of cell signaling pathways Nat. Cell Biol. 8 2006 1195 1203 (Pubitemid 44660581)
5. K. Jaqaman, and G. Danuser Linking data to models: data regression Nat. Rev. Mol. Cell Biol. 7 2006 813 819 (Pubitemid 44627474)
6. B.N. Kholodenko, and A. Kiyatkin 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
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 (Pubitemid 34874536)
8. T.S. Gardner, and D. di Bernardo J.J. Collins Inferring genetic networks and identifying compound mode of action via expression profiling Science 301 2003 102 105 (Pubitemid 36801571)
9. J. Stark, R. Callard, and M. Hubank From the top down: towards a predictive biology of signaling networks Trends Biotechnol. 21 2003 290 293 (Pubitemid 36776703)
10. R.J. Prill, and J. Saez-Rodriguez G. Stolovitzky Crowdsourcing network inference: the DREAM predictive signaling network challenge Sci. Signal. 4 2011 mr7
11. Z. Chen, and T.B. Gibson M.H. Cobb MAP kinases Chem. Rev. 101 2001 2449 2476 (Pubitemid 35373029)
12. Y.D. Shaul, and R. Seger The MEK/ERK cascade: from signaling specificity to diverse functions Biochim. Biophys. Acta 1773 2007 1213 1226 (Pubitemid 47125968)
13. C.-Y. Huang, and J.E. Ferrell Jr. Ultrasensitivity in the mitogen-activated protein kinase cascade Proc. Natl. Acad. Sci. USA 93 1996 10078 10083 (Pubitemid 26314577)
14. A.R. Asthagiri, and D.A. Lauffenburger A computational study of feedback effects on signal dynamics in a mitogen-activated protein kinase (MAPK) pathway model Biotechnol. Prog. 17 2001 227 239 (Pubitemid 32663385)
15. C. Widmann, and S. Gibson G.L. Johnson Mitogen-activated protein kinase: conservation of a three-kinase module from yeast to human Physiol. Rev. 79 1999 143 180 (Pubitemid 29056951)
16. L. Bardwell, and X. Zou N.L. Komarova Mathematical models of specificity in cell signaling Biophys. J. 92 2007 3425 3441 (Pubitemid 46698635)
17. A.S. Futran, and A.J. Link S.Y. Shvartsman ERK as a model for systems biology of enzyme kinetics in cells Curr. Biol. 23 2013 R972 R979
18. G. Pearson, and F. Robinson M.H. Cobb Mitogen-activated protein (MAP) kinase pathways: regulation and physiological functions Endocr. Rev. 22 2001 153 183 (Pubitemid 32458157)
19. Ledford, H. 2013. First-in-class cancer drug approved to fight melanoma. http://blogs.nature.com/news/2013/05/first-in-class-cancer-drug-approved-to- fight-melanoma.html. Nature News Blog. Posted 30 May 2013, Accessed January 2014. Nature, International Weekly Journal of Science, Nature Publishing Group, Macmillan Publishers, London, UK. http://www.nature.com
20. B. Kholodenko, M.B. Yaffe, and W. Kolch Computational approaches for analyzing information flow in biological networks Sci. Signal. 5 2012 re1
21. B. Godsey Improved inference of gene regulatory networks through integrated Bayesian clustering and dynamic modeling of time-course expression data PLoS ONE 8 2013 e68358
22. S.D. Santos, P.J. Verveer, and P.I. Bastiaens Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate Nat. Cell Biol. 9 2007 324 330 (Pubitemid 46344612)
23. S. Prabakaran, and R.A. Everley J. Gunawardena Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributions Mol. Syst. Biol. 7 2011 482
24. M. Andrec, and B.N. Kholodenko E. Sontag Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy J. Theor. Biol. 232 2005 427 441 (Pubitemid 39575111)
25. A.A. Margolin, and I. Nemenman A. Califano ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context BMC Bioinformatics 7 Suppl 1 2006 S7
26. B. Barzel, and A.L. Barabási Network link prediction by global silencing of indirect correlations Nat. Biotechnol. 31 2013 720 725
27. S. Feizi, and D. Marbach M. Kellis Network deconvolution as a general method to distinguish direct dependencies in networks Nat. Biotechnol. 31 2013 726 733
28. U.S. Bhalla, P.T. Ram, and R. Iyengar MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network Science 297 2002 1018 1023 (Pubitemid 34856036)
29. K. Lorenz, M.J. Lohse, and U. Quitterer Protein kinase C switches the Raf kinase inhibitor from Raf-1 to GRK-2 Nature 426 2003 574 579 (Pubitemid 37522645)
30. M. Cirit, C.C. Wang, and J.M. Haugh Systematic quantification of negative feedback mechanisms in the extracellular signal-regulated kinase (ERK) signaling network J. Biol. Chem. 285 2010 36736 36744
31. J. Saez-Rodriguez, A. Kremling, and E. Gilles Dissecting the puzzle of life: modularization of signal transduction networks Comput. Chem. Eng. 29 2005 619 629 (Pubitemid 40417807)
32. D. Del Vecchio, A.J. Ninfa, and E.D. Sontag Modular cell biology: retroactivity and insulation Mol. Syst. Biol. 4 2008 161
33. A.C. Ventura, J.A. Sepulchre, and S.D. Merajver A hidden feedback in signaling cascades is revealed PLOS Comput. Biol. 4 2008 e1000041
34. K.H. Kim, and H.M. Sauro Measuring retroactivity from noise in gene regulatory networks Biophys. J. 100 2011 1167 1177
35. R.P. Alexander, and P.M. Kim M.B. Gerstein Understanding modularity in molecular networks requires dynamics Sci. Signal. 2 2009 pe44
36. S. Jayanthi, K.S. Nilgiriwala, and D. Del Vecchio Retroactivity controls the temporal dynamics of gene transcription ACS Synth. Biol 2 2013 431 441
37. A.J. Bardwell, M. Abdollahi, and L. Bardwell Docking sites on mitogen-activated protein kinase (MAPK) kinases, MAPK phosphatases and the Elk-1 transcription factor compete for MAPK binding and are crucial for enzymic activity Biochem. J. 370 2003 1077 1085 (Pubitemid 36399103)
38. N. Blüthgen, and F.J. Bruggeman B.N. Kholodenko Effects of sequestration on signal transduction cascades FEBS J. 273 2006 895 906
39. P. Jiang, and A.C. Ventura D. Del Vecchio Load-induced modulation of signal transduction networks Sci. Signal. 4 2011 ra67
40. Y. Kim, and Z. Paroush S.Y. Shvartsman Substrate-dependent control of MAPK phosphorylation in vivo Mol. Syst. Biol. 7 2011 467
41. S.A. Gerber, and J. Rush S.P. Gygi Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS Proc. Natl. Acad. Sci. USA 100 2003 6940 6945 (Pubitemid 36706372)
42. D. Angeli, and E. Sontag Translation-invariant monotone systems, and a global convergence result for enzymatic futile cycles Nonlin. Anal. B Real World App. 9 2008 128 140 (Pubitemid 47562891)
43. G. Russo, M. di Bernardo, and E.D. Sontag Global entrainment of transcriptional systems to periodic inputs PLOS Comput. Biol. 6 2010 e1000739
44. J.P. Barton, and E.D. Sontag The energy costs of insulators in biochemical networks Biophys. J. 104 2013 1380 1390
45. Y. Xu, and J. Gunawardena Realistic enzymology for post-translational modification: zero-order ultrasensitivity revisited J. Theor. Biol. 311 2012 139 152
46. L. Wang, and E.D. Sontag On the number of steady states in a multiple futile cycle J. Math. Biol. 57 2008 29 52
47. M. Thomson, and J. Gunawardena Unlimited multistability in multisite phosphorylation systems Nature 460 2009 274 277