Bayesian analysis of signaling networks governing embryonic stem cell fate decisions

Bioinformatics

Volumn 21, Issue 6, 2005, Pages 741-753

  Woolf, Peter J ^a   Prudhomme, Wendy ^b   Daheron, Laurence ^c   Daley, George Q ^b   Lauffenburger, Douglas A ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FIBRONECTIN; LAMININ; LEUKEMIA INHIBITORY FACTOR; MITOGEN ACTIVATED PROTEIN KINASE; PROTEIN KINASE B; RAF PROTEIN; STAT3 PROTEIN;

ANIMAL CELL; ARTICLE; BAYES THEOREM; CELL COUNT; CELL DIFFERENTIATION; CELL FATE; CELL FUNCTION; CELL POPULATION; CELL PROLIFERATION; CELL RENEWAL; COMPUTER PROGRAM; CONTROLLED STUDY; EMBRYONIC STEM CELL; MATHEMATICAL COMPUTING; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; SIGNAL TRANSDUCTION; VALIDATION PROCESS; WESTERN BLOTTING;

EID: 15944426084     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti056     Document Type: Article

References (57)

1. Balasubramanian,S., Efimova,T. and Eckert,R.L. (2002) Green tea polyphenol stimulates a Ras, MEKK1, MEK3, and p38 cascade to increase activator protein 1 factor-dependent involucrin gene expression in normal human keratinocytes. J. Biol. Chem., 277, 1828-1836.
2. Beer,M.A. and Tavazoie,S. (2004) Predicting gene expression from sequence. Cell, 117, 185-198.
3. Burns,M.A., Johnson,B.N., Brahmasandra,S.N., Handique,K., Webster,J.R., Krishnan,M., Sammarco,T.S., Man,P.M., Jones,D., Heldsinger,D., Mastrangelo,C.H. and Burke,D.T. (1998) An integrated nanoliter DNA analysis device. Science, 282, 484-487.
4. Cagney,G., Uetz,P. and Fields,S. (2000) High-throughput screening for protein-protein interactions using two-hybrid assay. Methods Enzymol., 328, 3-14.
5. Chickering,D.M. (1996) Learning Bayesian networks is NP-complete. In Fisher,D. and Lenz,H.J. (eds), Learning from Data: Artificial Intelligence and Statistics V. Springer-Verlag, Vol. 112, pp. 121-130.
6. Cooper,G.F. and Herskovits,E. (1992) A Bayesian method for the induction of probabilistic networks from data. Machine Learn., 9, 309-347.
7. Cooper,G.F. and Yoo,C. (1999) Causal discovery from a mixture of experimental and observational data. Proceedings of the Fifteenth Conference on Uncertainty in Artificial Intelligence, Stockholm, Sweden, July 30-August 1. Morgan Kaufmann, San Mateo, CA.
8. Cox,A.D. and Der,C.J. (2003) The dark side of Ras: regulation of apoptosis. Oncogene, 22, 8999-9006.
9. Craxton,A., Shu,G., Graves,J.D., Saklatvala,J., Krebs,E.G. and Clark,E.A. (1998) p38 MAPK is required for CD40-induced gene expression and proliferation in B lymphocytes. J. Immunol., 161 3225-3236.
10. Decker,T. and Kovarik,P. (2000) Serine phosphorylation of STATs. Oncogene, 19, 2628-2637.
11. Ernst,M., Oates,A. and Dunn,A.R. (1996) Gp130-mediated signal transduction in embryonic stem cells involves activation of Jak and Ras/mitogen-activated protein kinase pathways. J. Biol. Chem., 271, 30136-30143.
12. Friedman,N. (2003) Probabilistic models for identifying regulation networks. Bioinformatics, 19 (Suppl. 2),II57.
13. Friedman,N., Goldszmidt,M. and Wyner,A. (1999) Data analysis with Bayesian networks: a bootstrap approach. Proceedings of the Fifteenth Conference on Uncertainty in Artificial Intelligence, Stockholm, Sweden, July 30-August 1, pp. 206-215.
14. Gansner,E. and North,S. (2003) neato.
15. 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.
16. Ghahramani,Z. (2001) An introduction to hidden Markov models and Bayesian networks. Intl. J. Pattern Recogn. Artif. Intell., 15, 9-42.
17. Grant,D.S., Kleinman,H.K. and Martin,G.R. (1990) The role of basement membranes in vascular development. Ann. N. Y. Acad. Sci., 588, 61-72.
18. Hartemink,A.J., Gifford,D.K., Jaakkola,T.S. and Young,R.A. (2002) Combining location and expression data for principled discovery of genetic regulatory network models. Pac. Symp. Biocomput., 437-449.
19. Heckerman,D. (1999) Learning in Graphical Models. MIT Press, Cambridge, MA.
20. Holland,J.H. (1995) Hidden Order: How Adaptation Builds Complexity. Perseus Publishing, NY.
21. Hsu,W.H., Joehannes,R., Thornton,J.A., Perry,B.B., Haverkamp,L.M., Gettings,N.D. and Guo,H. (2003) Bayesian Network tools in Java (BNJ) v2, Kansas State University Laboratory for Knowledge Discovery in Databases.
22. Janes,K.A., Kelly,J.R., Gaudet,S. Albeck,J.G. Sorger,P.K. and Lauffenburger,D.A. (2004) Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of the dynamic multivariate data. J. Comput. Biol., (in press).
23. Jensen,F.V. (1998) An Introduction to Bayesian Networks University College London Press, London.
24. Jeong,H. and Tombor,B. (2000) The large-scale organization of metabolic networks. Nature, 407, 651-654.
25. Johnson,G.L. and Lapadat,R. (2002) Mitogen-activated protein kinase pathways mediated by ERK, JNK, and p38 protein kinases. Science 298, 1911-1912.
26. Kitano,H. (2002) Computational systems biology. Nature, 420, 206-210.
27. Kozlov,A. and Koller,D. (1997) Nonuniform dynamic discretization in hybrid networks. Proceedings of the 13th Annual Conference on Uncertainty in Artificial Intelligence, Providence, RI.
28. Lund-Johansen,F., Davis,K., Bishop,J. and de Waal Malefyt,R. (2000) Flow cytometric analysis of immunoprecipitates: high-throughput analysis of protein phosphorylation and protein-protein interactions. Cytometry, 39, 250-259.
29. Maliakal,J.C. (2002) Quantitative high throughput endothelial cell migration and invasion assay system. Methods Enzymol., 352 175-182.
30. Matsuda,T., Nakamura,T., Nakao,K., Arai,T., Katsuki,M., Heike,T. and Yokota,T. (1999) STAT3 activation is sufficient to maintain an undifferentiated state of mouse embryonic stem cells. EMBO J., 18, 4261-4269.
31. Mavroudi,S., Papadimitriou,S. and Bezerianos,A. (2002) Gene expression data analysis with a dynamically extended self-organized map that exploits class information. Bioinformatics, 18, 1446-1453.
32. Morand,K.L., Burt,T.M., Regg,B.T. and Tirey,D.A. (2001) Advances in high-throughput mass spectrometry. Curr Opin. Drug Discov. Devel. 4, 729-735.
33. Neapolitan,R.E. (2003) Learning Bayesian Networks. Prentice Hall, Harlow.
34. Niwa,H., Burdon,T., Chambers,I. and Smith,A. (1998) Self-renewal of pluripotent embryonic stem cells is mediated via activation of STAT3. Genes Dev., 12, 2048-2060.
35. Noda,S., Kishi,K., Yuasa,T., Hayashi,H., Ohnishi,T., Miyata,I., Nishitani,H. and Ebina,Y. (2000) Overexpression of wild-type Akt1 promoted insulin-stimulated p70S6 kinase (p70S6K) activity and affected GSK3 beta regulation, but did not promote insulin-stimulated GLUT4 translocation or glucose transport in L6 myotubes. J. Med. Invest., 47, 47-55.
36. Ogasawara,T., Yasuyama,M. and Kawauchi,K. (2003) Constitutive activation of extra-cellular signal-regulated kinase and p38 mitogen-activated protein kinase in B-cell lymphoproliferative disorders. Int. J. Hematol., 77, 364-370.
37. Oh,H., Fujio,Y., Kunisada,K., Hirota.H., Matsui,H., Kishimoto,T. and Yamauchi-Takihara,K. (1998) Activation of phosphatidylinositol 3-kinase through glycoprotein 130 induces protein kinase B and p70 S6 kinase phosphorylation in cardiac myocytes. J. Biol. Chem., 273, 9703-9710.
38. Park,J.H., Kim,S.J., Oh,E.J., Moon,S.Y., Roh,S.I., Kim,C.G. and Yoon,H.S. (2003) Establishment and maintenance of human embryonic stem cells on STO, a permanently growing cell line. Biol. Reprod., 69, 2007-2014.
39. Pearl,J. (1988) Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference. Morgan Kaufmann Publishers, San Mateo, CA.
40. Pearl,J. (2000) Causality: Models, Reasoning, and Inference. Cambridge University Press, New York, Cambridge, UK.
41. Pearson,G., English,J.M., White,M.A. and Cobb,M.H. (2001) ERK5 and ERK2 cooperate to regulate NF-kappaB and cell transformation. J. Biol. Chem., 276, 7927-7931.
42. Price,N.D., Papin,J.A., Schilling,C.H. and Palsson,B.O. (2003) Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol., 21, 162-169.
43. Prudhomme,W. (2003) Quantitative Analysis of Mouse Embryonic Stem Cell Self-renewal versus Differentiation Responses to Cytokine and Extracellular Matrix Stimuli. MIT Press.
44. Prudhomme,W., Daley,G.Q., Zandstra,P. and Lauffenburger,D.A. (2004a) Multivariate proteomic analysis of murine embryonic stem cell self-renewal versus differentiation signaling. Proc. Natl. Acad. Sci. USA, 101, 2900-2905.
45. Prudhomme,W., Duggar,K.H. and Lauffenburger,D.A. (2004b) Cell population dynamics model for deconvolution of murine embryonic stem cell self-renewal and differentiation responses to cytokines and extracellular matrix. Biotechnol. Bioeng., 88, 264-272.
46. Raz,R., Lee,C.K., Cannizzaro,L.A., d'Eustachio,P. and Levy,D.E. (1999) Essential role of STAT3 for embryonic stem cell pluripotency. Proc. Natl Acad. Sci. USA, 96, 2846-2851.
47. Recio,J.A. and Merlino,G. (2002) Hepatocyte growth factor/scatter factor activates proliferation in melanoma cells through p38 MAPK, ATF-2 and cyclin D1. Oncogene, 21, 1000-1008.
48. 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.
49. Schiemann,W.P., Graves,L.M., Baumann,H., Morella,K.K., Gearing,D.P., Nielsen,M.D., Krebs,E.G. and Nathanson,N.M. (1995) Phosphorylation of the human leukemia inhibitory factor (LIF) receptor by mitogen-activated protein kinase and the regulation of LIF receptor function by heterologous receptor activation. Proc. Natl Acad. Sci. USA, 92, 5361-5365.
50. Smith,A.G., Heath,J.K., Donaldson,D.D., Wong,G.G., Moreau,J., Stahl,M. and Rogers,D. (1988) Inhibition of pluripotential embryonic stem cell differentiation by purified polypeptides. Nature, 336, 688-690.
51. Suriyapperuma,S.P., Lozovatsky,L., Ciciotte,S.L., Peters,L.L. and Gilligan,D.M. (2000) The mouse adducin gene family: alternative splicing and chromosomal localization. Mamm. Genome, 11, 16-23.
52. Takikawa,M., D'Ambrosio,B. et al. (2002) Real-time inference with large-scale temporal Bayes nets. Proceedings of the Eighteenth Annual Conference on Uncertainty in Artificial Intelligence San Francisco, CA.
53. Tong,S. and Koller,D. (2001) Active learning for structure in bayesian networks. Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence, Seattle, WA.
54. Vaudry,D., Stork,P.J., Lazarovici,P. and Eiden,L.E. (2002) Signaling pathways for PC12 cell differentiation: making the right connections. Science, 296, 1648-1649.
55. Williams,R.L., Hilton,D.J., Pease,S., Willson,T.A., Stewart,C.L., Gearing,D.P., Wagner,E.F., Metcalf,D., Nicola,N.A. and Gough,N.M. (1988) Myeloid leukaemia inhibitory factor maintains the developmental potential of embryonic stem cells. Nature, 336, 684-687.
56. Xu,S., Robbins,D., Frost,J., Dang,A., Lange-Carter,C. and Cobb,M.H. (1995) MEKK1 phosphorylates MEK1 and MEK2 but does not cause activation of mitogen-activated protein kinase. Proc. Natl. Acad. Sci. USA, 92, 6808-6812.
57. Zandstra,P.W., Le,H.V., Daley,G.Q., Griffith,L.G. and Lauffenburger,D.A. (2000) Leukemia inhibitory factor (LIF) concentration modulates embryonic stem cell self-renewal and differentiation independently of proliferation. Biotechnol. Bioeng., 69, 607-617.