Gene perturbation and intervention in probabilistic Boolean networks

Bioinformatics

Volumn 18, Issue 10, 2002, Pages 1319-1331

  Shmulevich, Ilya ^a   Dougherty, Edward R ^b   Zhang, Wei ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; INFORMATION SCIENCE; MATHEMATICAL COMPUTING; MATHEMATICAL GENETICS; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROBABILITY; SIMULATION; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETIC ENGINEERING; GENETICS; HUMAN GENOME PROJECT; METHODOLOGY; MUTAGENESIS; MUTATION; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STATISTICAL MODEL; STATISTICS;

CHROMOSOME MAPPING; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETIC ENGINEERING; HUMAN GENOME PROJECT; MODELS, GENETIC; MODELS, STATISTICAL; MUTAGENESIS; MUTATION; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; STOCHASTIC PROCESSES;

EID: 0036772705     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.10.1319     Document Type: Article

References (42)

1. Abrahams,P.J. and Van der Eb,A.J. (1975) In vitro transformation of rat and mouse cells by DNA from simian virus 40. J. Virol., 16, 206-209.
2. Altenberg,L. (1994) The evolution of evolvability in genetic programming. In Kinnear,K.E. (ed.), Advances in Genetic Programming. MIT Press, Cambridge, MA, pp. 47-74.
3. Bargonetti,J., Reynisdottir,I., Friedman,P. and Prives,C. (1992) Site-specific binding of wild-type p53 to cellular DNA is inhibited by SV40 T antigen and mutant p53. Genes Dev., 6, 1886-1898.
4. Bouvet,M., Bold,R.J., Lee,J., Evans,D.B., Abbruzzese,J.L., Chiao,P.J., McConkey,D.J., Chandra,J., Chada,S., Fang,B. and Roth,J.A. (1998) Adenovirus-mediated wild-type p53 tumor suppressor gene therapy induces apoptosis and suppresses growth of human pancreatic cancer. Ann. Surg. Oncol., 5, 681-688.
5. Brinster,R.L., Chen,H.Y, Messing,A., van Dyke,T., Levine,A.J. and Palmiter,R.D. (1984) Transgenic mice harboring SV40 T-antigen genes develop characteristic brain tumors. Cell, 37, 367-379.
6. Carbone,M., Rizzo,P. and Pass,H.I. (1997) Simian virus 40, polio-vaccines and human tumors: a review of recent developments. Oncogene, 15, 1877-1888.
7. Cho,G.E. and Meyer,C.D. (2000) Markov chain sensitivity measured by mean first passage times. Linear Algebra and Its Applications, 316, 21-28.
8. Çinlar,E. (1997) Introduction to Stochastic Processes. Prentice Hall, Englewood, NJ.
9. DeCaprio,J.A., Ludlow,J.W., Figge,J., Shew,J.Y., Huang,C.M., Lee,W.H., Marsilio,E., Paucha,E. and Livingston,D.M. (1988) SV40 large tumor antigen forms a specific complex with the product of the retinoblastoma susceptibility gene. Cell, 54, 275-283.
10. Donehower,L.A., Harvey,M., Slagle,B.L., McArthur,M.J., Montgomery,Jr,C.A., Butel,J.S. and Bradley,A. (1992) Mice deficient for p53 are developmentally normal but susceptible to spontaneous tumours. Nature, 356, 215-221.
11. Dougherty,E.R., Kim,S. and Chen,Y. (2000) Coefficient of determination in nonlinear signal processing. Signal Process., 80, 2219-2235.
12. El-Deiry,W.S., Tokino,T., Velculescu,V.E., Levy,D.B., Parsons,R., Trent,J.M., Lin,D., Mercer,W.E., Kinzler,K.W. and Vogelstein,B. (1993) WAF1, a potential mediator of p53 tumor suppression. Cell, 75, 817-825.
13. Glass,K. and Kauffman,S.A. (1973) The logical analysis of continuous, non-linear biochemical control networks. J Theor. Biol., 39, 103-129.
14. Goldberg,D. (1989) Genetic Algorithms in Search, Optimization, and Machine Learning. Addison-Wesley, Reading, MA.
15. Harley,C.B. (1991) Telomere loss: mitotic clock or genetic time bomb? Mutation Res., 256, 271-282.
16. Hiyama,E., Hiyama,K., Yokoyama,T., Matsuura,Y., Piatyszek,M.A. and Shay,J.W. (1995) Correlating telomerase activity levels with human neuroblastoma outcomes. Nat. Med., 1, 249-255.
17. Hogenesch,J.B., Ching,K.A., Batalov,S., Su,A.I., Walker,J.R., Zhou,Y., Kay,S.A., Schultz,P.G. and Cooke,M.P. (2001) A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell, 106, 413-415.
18. Hollstein,M., Sidransky,D., Vogelstein,B. and Harris,C.C. (1991) p53 mutations in human cancers. Science, 253, 49-53.
19. Huang,S. (1999) Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery. J. Mol. Med., 77, 469-480.
20. Huang,S. and Ingber,D.E. (2000) Regulation of cell cycle and gene activity patterns by cell shape: evidence for attractors in real regulatory networks and the selective mode of cellular control. InterJournal Genetics, MS: 238, http://www.interjournal.org
21. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
22. Kauffman,S.A. (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor Biol., 22, 437-467.
23. Kauffman,S.A. (1993) The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, Oxford.
24. Kauffman,S.A. and Levin,S. (1987) Towards a general theory of adaptive walks on rugged landscapes. J. Theor Biol., 128, 11-45.
25. Kim,N.W., Piatyszek,M.A., Prowse,K.R., Harley,C.B., West,M.D., Ho,P.L.C., Coviello,G.M., Wright,W.E., Weinrich,S.L. and Shay,J.W. (1994) Specific association of human telomerase activity with immortal cells and cancer. Science, 266, 2011-2015.
26. Kim,S., Dougherty,E.R., Chen,Y., Sivakumar,K., Meltzer,P., Trent,J.M. and Bittner,M. (2000a) Multivariate measurement of gene expression relationships. Genomics, 67, 201-209.
27. Kim,S., Dougherty,E.R., Bittner,M.L., Chen,Y., Sivakumar,K., Meltzer,P. and Trent,J.M. (2000b) General nonlinear framework for the analysis of gene interaction via multivariate expression arrays. J .Biomed. Optics, 5, 411-424.
28. Kobayashi,T., Ruan,S.-B., Jabbur,J.R., Consoli,U., Clodi,K., Shiku,H., Owen-Schaub,L., Andreeff,M., Reed,J. and Zhang,W. (199) Differential p53 phosphorylation and activation of apoptosis-promoting genes Bax and Fas/APO-1 by radiation and ara-C treatment. Cell Death and Differentiation, 85, 584-591.
29. Kouhata,T., Fukuyama,K., Hagihara,N. and Tabuchi,K. (2001) Detection of simian virus 40 DNA sequence in human primary glioblastomas multiforme. J. Neurosurg., 95, 96-101.
30. Lowe,S.W., Schmitt,E.M., Smith,S.W., Osborne.,B.A. and Jacks,T. (1993) p53 is required for radiation-induced apoptosis in mouse thymocytes. Nature, 362, 847-849.
31. Miyashita,T. and Reed,J.C. (1995) Tumor suppressor p53 is a direct transcriptional activator of the human bax gene. Cell, 80, 293-299.
32. Owen-Schaub,L.B., Zhang,W., Cusack,J., Angelo,L.S., Santee,S.M., Fujiwara,T., Roth,J.A., Deisseroth,A.B., Zhang,W.-W., Kruzel,E. and Radinsky,R. (1995) Wild-type and a temperature-sensitive mutant of human p53 induce Fas/APO-1 expression. Mol. Cell. Biol., 15, 3032-3040.
33. Schweitzer,P.J. (1968) Perturbation theory and finite Markov chains. J. Appl. Probability, 5, 401-413.
34. Shmulevich.I., Dougherty,E.R., Kim,S. and Zhang,W. (2002) Probabilistic boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics, 18, 261-274.
35. Somogyi,R. and Sniegoski,C. (1996) Modeling the complexity of gene networks: understanding multigenic and pleiotropic regulation. Complexity, 1, 45-63.
36. Swisher,S.G., Roth,J.A., Nemunaitis,J., Lawrence,D.D., Kemp,B.L., Carrasco,C.H., Connors,D.G., El-Naggar,A.K., Fossella,F., Glisson,B.S. et al. (1999) Adenovirus-mediated p53 gene transfer in advanced non-small-cell lung cancer. J. Natl Cancer Institute, 91, 763-771.
37. Szallasi,Z. and Liang,S. (1998) Modeling the normal and neoplastic cell cycle with realistic boolean genetic networks: their application for understanding carcinogenesis and assessing therapeutic strategies. Pac. Symp. Biocomput., 3, 66-76.
38. Thomas,R., Thieffry,D. and Kaufman,M. (1995) Dynamical behaviour of biological regulatory networks-I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bull. Math. Biol., 57, 247-276.
39. Wuensche,A. (1996) Discrete Dynamics Lab (DDLab), http://www. santafe.edu/~wuensch/ddlab.html.
40. Wuensche,A. (1998) Genomic regulation modeled as a network with basins of attraction. Pac. Symp. Biocomput., 3, 89-102.
41. Zhang,W., Piatyszek,M.A., Kobayashi,T., Estey,E., Andreeff,M., Deisseroth,A.B. and Shay,J.W. (1996) Detection of telomerase activity in human acute myelogenous leukemia and modulation of the activity by differentiation-inducing agents. Clin. Cancer Res., 2, 799-803.
42. Zhu,J., Abate,M., Rice,P.W. and Cole,C. (1991) The ability of simian virus 40 large T antigen to immortalize primary mouse embryo fibroblasts cosegregates with its ability to bind p53. J. Virol., 65, 6872-6880.