Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

Molecular Systems Biology

Volumn 5, Issue , 2009, Pages

  Saez Rodriguez, Julio ^a,b,c   Alexopoulos, Leonidas G ^a,b,c,e   Epperlein, Jonathan ^a,b   Samaga, Regina ^d   Lauffenburger, Douglas A ^a,c   Klamt, Steffen ^d   Sorger, Peter K ^a,b,c  

^a Center for Cell Decision Processes   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c Massachusetts Institute of Technology Cambridge   (United States)

^d MAX PLANCK INSTITUTE FOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS   (Germany)

^e NATIONAL TECHNICAL UNIVERSITY OF ATHENS   (Greece)

Author keywords

Logical modelling; Protein networks; Signal transduction

Indexed keywords

CYTOKINE; PROTEIN;

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; CYTOKINE PRODUCTION; INFORMATION SCIENCE; LIVER CELL; MEDICAL LITERATURE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; SIGNAL TRANSDUCTION; BIOLOGICAL MODEL; BIOLOGY; CYTOLOGY; HUMAN; LIVER;

MAMMALIA;

COMPUTATIONAL BIOLOGY; CYTOKINES; HUMANS; LIVER; MODELS, BIOLOGICAL; PROTEINS; SIGNAL TRANSDUCTION; SOFTWARE;

EID: 71449120701     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2009.87     Document Type: Article

References (78)

1. Akaike H (1974) A new look at the statistical model identification. Automat Contr 19: 716-723
2. Aldridge B, Saez-Rodriguez J, Muhlich J, Sorger P, Lauffenburger DA (2009) Fuzzy logic analysis of kinase pathway crosstalk inTNF/ EGF/insulin-induced signaling. PLoS Comput Biol 5: e1000340
3. Aldridge BB, Burke JM, Lauffenburger DA, Sorger PK (2006) Physicochemical modelling of cell signalling pathways. Nat Cell Biol 8: 1195-1203
4. Bader G, Cary MP, Sander C (2006) Pathguide: a pathway resource list. Nucleic Acids Res 34: D504-D506
5. Bansal M, Belcastro V, Ambesi-Impiombato A, Di Bernardo D (2007) How to infer gene networks from expression profiles. Mol Syst Biol 3: 78
6. Barabási AL, Oltvai Z (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113
7. Barron A, Rissanen J, Yu B (1998) The minimum description length principle in coding and modeling. IEEE Transactions on Information Theory 44: 2743-2760
8. Bauer-Mehren A, Furlong LI, Sanz F (2009) Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Mol Syst Biol 5: 290
9. Bollobas B (1986) Combinatorics: Set Systems, Hypergraphs, Families of Vectors, and Combinatorial Probability. Cambridge, UK: Cambridge University Press
10. Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V (2006) The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol 7: R36
11. Bossi A, Lehner B (2009) Tissue specificity and the human protein interaction network. Mol Syst Biol 5: 260
12. Chaouiya C, Remy E, Thieffry D (2008) Petri net modelling of biological regulatory networks. J Disc Algorithms 6: 165-177
13. Chatr-Aryamontri A, Ceol A, Palazzi L, Nardelli G, Schneider M, Castagnoli L, Cesareni G (2007) MINT: the Molecular INTeraction database. Nucleic Acids Res 35: D572-D574
14. Chaves M, Albert R, Sontag ED (2005) Robustness and fragility of Boolean models for genetic regulatory networks. J Theoret Biol 235: 431-449
15. Cho KH, Choo SM, Jung SH, Kim JR, Choi HS, Kim J (2007) Reverse engineering of gene regulatory networks. IET Syst Biol 1: 149-163
16. Chuang H, Lee E, Liu Y, Lee D, Ideker T (2007) Network-based classification of breast cancer metastasis. Mol Syst Biol 3: 10
17. Cusick M, Yu H, Smolyar A, Venkatesan K, Carvunis A, Simonis N, Rual J, Borick H, Braun P, Dreze M, Vandenhaute J, Galli M, Yazaki J, Hill D, Ecker J, Roth FP, Vidal M(2009) Literature-curated protein interaction datasets. Nat Methods 6: 39-46
18. D'haeseleer P, Liang S, Somogyi R (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 16: 707-726
19. De Jong H (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 9: 67-103
20. Fanger GR, Johnson NL, Johnson GL (1997) MEK kinases are regulated by EGF and selectively interact with Rac/Cdc42. EMBO J 16: 4961-4972
21. Fauré A, Naldi A, Chaouiya C, Thieffry D (2006) Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics 22: e124-e131
22. Fisher J, Henzinger T (2007) Executable cell biology. Nate Biotechnol 25: 1239-1249
23. Floyd RW (1962) Algorithm 97 (SHORTEST PATH). Commun ACM 5: 345
24. Gat-Viks I, Shamir R (2007) Refinement and expansion of signaling pathways: the osmotic response network in yeast. Genome Res 17: 358-367
25. Gaudet S, Janes KA, Albeck JG, Pace EA, Lauffenburger DA, Sorger PK (2005) A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol Cell Proteomics 4: 1569-1590
26. Goldberg DE (1989) Genetic Algorithms in Search, Optimization, and Machine Learning. Boston, MA, USA: Addison-Wesley Professional
27. Guan KL, Figueroa C, Brtva TR, Zhu T, Taylor J, Barber TD, Vojtek AB (2000) Negative regulation of the serine/threonine kinase B-Raf by Akt. J Biol Chem 275: 27354-27359
28. Gupta S, Bisht SS, Kukreti R, Jain S, Brahmachari SK (2007) Boolean network analysis of a neurotransmitter signaling pathway. J Theoret Biol 244: 463-469
29. Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100: 57-70
30. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M et al (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-D261
31. Herbst RS (2002) ZD1839: targeting the epidermal growth factor receptor in cancer therapy. Expert Opin Invest Drugs 11: 837-849
32. Hers I, Tavaré JM (2005) Mechanism of feedback regulation of insulin receptor substrate-1 phosphorylation in primary adipocytes. Biochem J 388: 713-720
33. Hotamisligil GS, Peraldi P, Budavari A, Ellis R, White MF, Spiegelman BM (1996) IRS-1-mediated inhibition of insulin receptor tyrosine kinase activity in TNF-alpha- and obesity-induced insulin resistance. Science 271: 665-668
34. Hotte SJ, Hirte HW (2002) BAY 43-9006: early clinical data in patients with advanced solid malignancies. Curr Pharm Des 8: 2249-2253
35. Huang S, Ingber DE (2000) Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks. Exp Cell Res 261: 91-103
36. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302: 449-453
37. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32: D277-D280
38. Kauffman SA (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theoret Biol 22: 437-467
39. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B et al (2007) IntAct-open source resource for molecular interaction data. Nucleic Acids Res 35: D561-D565
40. Klamt S, Haus UU, Theis F (2009) Hypergraphs and cellular networks. PLoS Comput Biol 5: e1000385
41. Klamt S, Saez-Rodriguez J, Gilles ED (2007) Structural and functional analysis of cellular networks with Cell Net Analyzer. BMC Syst Biol 1: 2
42. Klamt S, Saez-Rodriguez J, Lindquist J, Simeoni L, Gilles ED (2006) A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics 7: 56
43. Köcher T, Superti-Furga G (2007) Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat Methods 4: 807-815
44. Kremling A, Saez-Rodriguez J (2007) Systems biology-an engineering perspective. J Biotechnol 129: 329-351
45. Laubenbacher R, Stigler B (2004) Acomputational algebra approach to the reverse engineering of gene regulatory networks. J Theoret Biol 229: 523-537
46. Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308-312
47. Ma'ayan A, Jenkins S, Neves S, Hasseldine A, Grace E, Dubin-Thaler B, Eungdamrong NJ, Weng G, Ram PT, Rice JJ, Kershenbaum A, Stolovitzky GA, Blitzer RD, Iyengar R (2005) Formation of regulatory patterns during signal propagation in a mammalian cellular network. Science 309: 1078-1083
48. MacBeath G, Schreiber SL (2000) Printing proteins as microarrays for high-throughput function determination. Science 289: 1760-1763
49. Marchetti L, Klein M, Schlett K, Pfizenmaier K, Eisel UL (2004) Tumor necrosis factor (TNF)-mediated neuroprotection against glutamateinduced excitotoxicity is enhanced by N-methyl-D-aspartate receptor activation. Essential role of a TNF receptor 2-mediated phosphatidylinositol 3-kinase-dependent NF-kappa B pathway. J Biol Chem 279: 32869-32881
50. Mendelson E (1970) Schaum's Outline of Boolean Algebra and Switching Circuits. New York: McGraw-Hill
51. Mendoza L, Xenarios I (2006) A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor Biol Med Modelling 3: 13
52. Mitchell M (1998) An Introduction to Genetic Algorithms. Cambridge, MA, USA: MIT Press
53. Nelander S, Wang W, Nilsson B, She Q, Pratilas C, Rosen N, Gennemark P, Sander C (2008) Models from experiments: combinatorial drug perturbations of cancer cells. Mol Syst Biol 4: 11
54. Ozes ON, Akca H, Mayo LD, Gustin JA, Maehama T, Dixon JE, Donner DB (2001) A phosphatidylinositol 3-kinase/Akt/mTOR pathway mediates and PTEN antagonizes tumor necrosis factor inhibition of insulin signaling through insulin receptor substrate-1. Proc Natl Acad Sci USA 98: 4640-4645
55. Perkins TJ, Jaeger J, Reinitz J, Glass L (2006) Reverse engineering the gap gene network of Drosophila melanogaster. PLoS Comput Biol 2: e51
56. Pieroni E, De La Fuente Van Bentem S, Mancosu G, Capobianco E, Hirt H, De La Fuente A (2008) Protein networking: insights into global functional organization of proteomes. Proteomics 8: 799-816
57. Pujana M, Han J, Starita L, Stevens K, Tewari M, Ahn J, Rennert G, Moreno V, Kirchhoff T, Gold B, Assmann V, Elshamy W, Rual J, Levine D, Rozek L, Gelman R, Gunsalus K, Greenberg R, Sobhian B, Bertin N et al (2007) Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet 39: 1338-1349
58. Rhee SH, Keates AC, Moyer MP, Pothoulakis C (2004) MEK is a key modulator for TLR5-induced interleukin-8 and MIP3alpha gene expression in non-transformed human colonic epithelial cells. J Biol Chem 279: 25179-25188
59. Rual J, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV,Wong SL, Franklin G, Li S et al (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178
60. Russell M, Lange-Carter CA, Johnson GL (1995) Direct interaction between Ras and the kinase domain of mitogen-activated protein kinase kinase kinase (MEKK1). J Biol Chem 270: 11757-11760
61. Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP (2005) Causal protein-signaling networks derived from multiparameter single-cell data. Science 308: 523-529
62. Saez-Rodriguez J, Goldsipe A, Muhlich J, Alexopoulos LG, Millard B, Lauffenburger DA, Sorger PK (2008) Flexible informatics for linking experimental data to mathematical models via DataRail. Bioinformatics 24: 840-847
63. Saez-Rodriguez J, Mirschel S, Hemenway R, Klamt S, Gilles ED, Ginkel M (2006) Visual setup of logical models of signaling and regulatory networks with ProMoT. BMC Bioinformatics 7: 506
64. Saez-Rodriguez J, Simeoni L, Lindquist JA, Hemenway R, Bommhardt U, Arndt B, Haus UU,Weismantel R, Gilles ED, Klamt S, Schraven B (2007) A logical model provides insights into T cell receptor signaling. PLoS Comput Biol 3: e163
65. Saltiel A, Kahn C (2001) Insulin signalling and the regulation of glucose and lipid metabolism. Nature 414: 799-806
66. Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S (2009) The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Comp Biol 5: e1000438
67. Schwarz G (1978) Estimating the dimension of a model. Ann Stat 6: 461-464
68. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504
69. Shmulevich I, Dougherty ER, Kim S, Zhang W (2002) Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18: 261-274 (Pubitemid 34183104)
70. Taylor IW, Linding R,Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, Wrana JL (2009) Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol 27: 199-204
71. Thomas R, D'Ari R (1990) Biological Feedback. Boca Raton, FL, USA: CRC Press
72. Thomas R, Kaufman M (2001) Multistationarity, the basis of cell differentiation and memory. II. Logical analysis of regulatory networks in terms of feedback circuits. Chaos (Woodbury, NY) 11: 180-195
73. Tibshirani R (1994) Regression shrinkage and selection via the lasso. J R Stat Soc B 58: 267-288
74. Wittmann D, Krumsiek J, Saez-Rodriguez J, Lauffenburger DA, Klamt S, Theis F (2009) From qualitative to quantitative modeling. BMC Systems Biol 3: 98
75. Yaguchi S, Fukui Y, Koshimizu I, Yoshimi H, Matsuno T, Gouda H, Hirono S, Yamazaki K, Yamori T (2006) Antitumor activity of ZSTK474, a new phosphatidylinositol 3-kinase inhibitor. J Natl Cancer Inst 98: 545-556
76. Zhang R, Shah M, Yang J, Nyland S, Liu X, Yun J, Albert R, Loughran T (2008) Network model of survival signaling in large granular lymphocyte leukemia. Proc Natl Acad Sci USA 105: 16308
77. Zhao W, Serpedin E, Dougherty ER (2006) Inferring gene regulatory networks from time series data using the minimum description length principle. Bioinformatics 22: 2129-2135
78. Zhou D, He Y (2008) Extracting interactions between proteins fromthe literature. J Biomed Informatics 41: 393-407