Application of Bayesian networks for inferring cause-effect relations from gene expression profiles of cancer versus normal cells

Mathematical Biosciences

Volumn 209, Issue 2, 2007, Pages 528-546

  Polanski, Andrzej ^a   Polanska, Joanna ^a   Jarzab, Michal ^b   Wiench, Malgorzata ^b   Jarzab, Barbara ^b  

^a SILESIAN UNIVERSITY OF TECHNOLOGY   (Poland)

^b INSTITUTE OF ONCOLOGY   (Poland)

Author keywords

Applied statistics; Bayesian networks; Cancer; Cause effect relations; DNA microarrays

Indexed keywords

CELLS; DNA; GENE EXPRESSION; MATHEMATICAL MODELS; MICROARRAYS; PROBABILITY DISTRIBUTIONS; STATISTICS; TUMORS;

APPLIED STATISTICS; CAUSE-EFFECT RELATIONS; DNA MICROARRAYS;

BAYESIAN NETWORKS;

BAYESIAN ANALYSIS; CANCER; EXPERIMENTAL STUDY; GENE EXPRESSION; GENETIC ANALYSIS;

ARTICLE; BAYES THEOREM; CANCER CELL; CELL DIFFERENTIATION; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION PROFILING; HUMAN; HUMAN CELL; HUMAN TISSUE; MALIGNANT TRANSFORMATION; MATHEMATICAL MODEL; MEASUREMENT; THYROID PAPILLARY CARCINOMA;

BAYES THEOREM; CARCINOMA, PAPILLARY; CELL TRANSFORMATION, NEOPLASTIC; GENE EXPRESSION PROFILING; HUMANS; LIKELIHOOD FUNCTIONS; MATHEMATICS; MODELS, GENETIC; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; THYROID NEOPLASMS;

EID: 34548565986     PISSN: 00255564     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mbs.2007.03.006     Document Type: Article

References (28)

1. Aldred M.A., et al. Papillary and follicular thyroid carcinomas show distinctly different microarray expression profiles and can be distinguished by a minimum of five genes. J. Clin. Oncol. 22 17 (2004) 3531-3539
2. Beer D.G., Kardia S.L., Huang C.C., Giordano T.J., Levin A.M., Misek D.E., Lin L., Chen G., Gharib T.G., Thomas D.G., Lizyness M.L., Kuick R., Hayasaka S., Taylor J.M., Iannettoni M.D., Orringer M.B., and Hanash S. Gene expression profiles predict survival of patients with lung adenocarcinoma. Nat. Med. 8 (2002) 816-824
3. Chickering D.M. Learning equivalence classes of Bayesian-network structures. J. Mach. Learn. Res. 2 (2002) 445-498
4. Ciampi R., Knauf J.A., Rabes H.M., Fagin J.A., and Nikiforov Y.E. BRAF kinase activation via chromosomal rearrangement in radiation-induced and sporadic thyroid cancer. Cell Cycle 4 4 (2005) 547-548
5. Cox D.R. Causality: some statistical aspects. J. R. Stat. Soc. Ser. A 155 (1992) 291-301
6. Fagin J.A. Challenging dogma in thyroid cancer molecular genetics-role of RET/PTC and BRAF in tumor initiation. J. Clin. Endocrinol. Metab. 89 (2004) 4264-4266
7. Frattini M., Ferrario C., Bressan P., Balestra D., De Cecco L., Mondellini P., Bongarzone I., Collini P., Gariboldi M., Pilotti S., Pierotti M.A., and Greco A. Alternative mutations of BRAF, RET and NTRK1 are associated with similar but distinct gene expression patterns in papillary thyroid cancer. Oncogene 23 (2004) 7436-7440
8. Friedman N., Linial M., Nachman I., and Pe'er D. Using Bayesian networks to analyze expression data. J. Comput. Biol. 7 3-4 (2004) 601-620
9. N. Friedman, The Bayesian structural EM algorithm, in: Fourteenth Conference on Uncertainty in Artificial Intelligence (UAI), 1998.
10. The Gene Ontology Consortium, Gene Ontology: tool for the unification of biology, Nat. Genet. 25 (2000) 25-29.
11. Giordano T.J., Kuick R., Thomas D.G., Misek D.E., Vinco M., Sanders D., Zhu Z., Ciampi R., Roh M., Shedden K., Gauger P., Doherty G., Thompson N.W., Hanash S., Koenig R.J., and Nikiforov Y.E. Molecular classification of papillary thyroid carcinoma: distinct BRAF, RAS, and RET/PTC mutation-specific gene expression profiles discovered by DNA microarray analysis. Oncogene 24 44 (2005) 6646-6656
12. Irizarry R.A., Hobbs B., Collin F., Beazer-Barclay Y.D., Antonellis K.J., Scherf U., and Speed T.P. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4 (2003) 249-264
13. Jarzab B., Wiench M., Fujarewicz K., Simek K., Jarzab M., Oczko-Wojciechowska M., Wloch J., Czarniecka A., Chmielik E., Lange D., Pawlaczek A., Szpak S., Gubala E., and Swierniak A. Gene expression profile of papillary thyroid cancer: sources of variability and diagnostic implications. Cancer Res. 65 (2005) 1587-1597
14. Jensen F.V. Bayesian Networks and Decision Graphs (2002), Springer
15. Metropolis N., Rosenbluth A.W., Rosenbluth M.N., Teller A.H., and Teller E. Equations of state calculations by fast computing machines. J. Chem. Phys. 21 (1953) 1087-1092
16. Mitsutake N., Knauf J.A., Mitsutake S., Mesa Jr. C., Zhang L., and Fagin J.A. Conditional BRAFV600E expression induces DNA synthesis, apoptosis, dedifferentiation, and chromosomal instability in thyroid PCCL3 cells. Cancer Res. 65 (2005) 2465-2473
17. Neapolitan R.E. Learning Bayesian Networks (2004), Prentice Hall
18. Pearl J. Causality: Models, Reasoning, and Inference (2000), Cambridge University Press
19. Pearl J., and Verma T.S. A theory of inferred causation. In: Allen J.A., Fikes R., and Sandewall E. (Eds). Principles of Knowledge Representation and Reasoning (1991), Morgan Kaufmann, San Mateo
20. Pe'er D., Regev A., Elidan G., and Friedman N. Inferring subnetworks from perturbed expression profiles. Bioinformatics 17 (2001) S215-S224
21. Polanska J., Borys D., and Polanski A. Node assignment problem in Bayesian networks. Int. J. Appl. Math. Comput. Sci. 16 2 (2006) 233-240
22. Rhodes D.R., Yu J., Shanker K., Deshpande N., Varambally R., Ghosh D., Barrette T., Pandey A., and Chinnaiyan A.M. ONCOMINE, a cancer microarray database and integrated data mining platform. Neoplasia 6 1 (2004) 1-6
23. D. Rusinek, J. Zebracka, M. Oczko-Wojciechowska, M. Wiench, D. Handkiewicz-Junak, G. Gala, K. Simek, K. Fujarewicz, Initiating mutations of BRAF gene in papillary thyroid carcinoma, in: Proceedings of the 31st Annual Meeting of the European Thyroid Association, Naples, 2006, p. 54.
24. Santoro M. Minireview: RET: normal and abnormal functions. Endocrinology 145 (2004) 5448-5451
25. Singh D., Febbo P.G., Ross K., Jackson D.G., Manola J., Ladd C., Tamayo P., Renshaw A.A., D'Amico A.V., Richie J.P., Lander E.S., Loda M., Kantoff P.W., Golub T.R., and Sellers W.R. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 1 (2002) 203-209
26. Viglietto G., Chiappetta G., Martinez-Tello F.J., Fukunaga F.H., Tallini G., Rigopoulou D., Visconti R., Mastro A., Santoro M., and Fusco A. RET/PTC oncogene activation is an early event in thyroid carcinogenesis. Oncogene 11 (1995) 1207-1210
27. Weinberg R.A. Cancer: a genetic disorder. In: Mendelsohn J., Howley P.M., Israel M.A., and Liotta L.A. (Eds). The Molecular Basis of Cancer (2001), WB Saunders 3-9
28. Wiench M., Wloch J., Oczko M., Gubala E., and Jarzab B. Papillary thyroid carcinoma: RET/PTC rearrangement as age-related lesion. Eur. J. Cancer 37 suppl. 6 (2001) S25