Data-driven approach to predict survival of cancer patients

IEEE Engineering in Medicine and Biology Magazine

Volumn 28, Issue 4, 2009, Pages 58-66

  Motakis, Efthimios ^c   Ivshina, Anna ^c   Kuznetsov, Vladimir ^a,b  

^a Division of Genome and Gene Expression Data Analysis   (Singapore)

^b BIOINFORMATICS INSTITUTE   (Singapore)

^c NONE

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CANCER PATIENT; CANCER SURVIVAL; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC ASSOCIATION; HIGH RISK POPULATION; HUMAN; MATHEMATICAL ANALYSIS; MICROARRAY ANALYSIS; NEOPLASM; PROGNOSIS;

ALGORITHMS; BREAST NEOPLASMS; CELL CYCLE; COHORT STUDIES; DATABASES, GENETIC; FEMALE; GENE EXPRESSION PROFILING; HUMANS; KAPLAN-MEIERS ESTIMATE; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; PROPORTIONAL HAZARDS MODELS; REGRESSION ANALYSIS; REPRODUCIBILITY OF RESULTS;

EID: 68049087729     PISSN: 07395175     EISSN: None     Source Type: Journal    
DOI: 10.1109/MEMB.2009.932937     Document Type: Article

References (23)

1. L. J. van't Veer, H. Dai, M. J. van de Vijver, Y. D. He, A. A. M. Hart, M. Mao, H. L. Peterse, K. van der Kooy, M. J. Marton, A. T. Witteveen, G. J. Schreiber, R. M. Kerkhoven, C. Roberts, P. S. Linsley, R. Bernards, and S. H. Friend, "Gene expression profiling predicts clinical outcome of breast cancer," Nature, vol. 415, no. 6871, pp. 530-536, 2002.
2. A. V. Ivshina, J. George, O. Senko, B. Mow, T. C. Putti, J. Smeds, T. Lindahl, Y. Pawitan, P. Hall, H. Nordgren, J. E. L. Wong, E. T. Liu, J. Bergh, V. A. Kuznetsov, and L. D. Miller, "Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer," Cancer Res., vol. 66, no. 21, pp. 10292-10301, 2006.
3. Y. Pawitan, J. Bjohle, L. Amler, A. L. Borg, S. Egyhazi, P. Hall, X. Han, L. Holmberg, F. Huang, S. Klaar, E. T. Liu, L. Miller, H. Nordgren, A. Ploner, K. Sandelin, P. M. Shaw, J. Smeds, L. Skoog, S. Wedren, and J. Bergh, "Gene expression profiling spares early breast cancer patients from adjuvant therapy: Derived and validated in two population-based cohorts," Breast Cancer Res., vol. 7, no. 6, pp. R953-R964, 2005.
4. E. Bair and R. Tibshirani, "Semi-supervised methods to predict patients survival from gene expression data," PLoS Biol., vol. 2, no. 4, pp. 511-521, 2004.
5. H. Y. Chang, D. S. Nuyten, J. B. Sneddon, T. Hastie, R. Tibshirani, T. Sorlie, H. Dai, Y. D. He, L. J. van't Veer, H. Bartelink, M. van de Rijn, P. O. Brown, and M. J. van de Vijner, "Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival," Proc. Nat. Acad. Sci. USA, vol. 102, no. 10, pp. 3738-3743, 2005.
6. S. Michiels, S. Koscielny, and K. Hill, "Prediction of cancer outcome with microarrays: A multiple random validation strategy," Lancet, vol. 365, no. 9458, pp. 488-492, 2005.
7. E. T. Liu, V. A. Kuznetsov, and L. D. Miller, "In the pursuit of complexity: Systems medicine in cancer biology," Cancer Cell, vol. 9, no. 4, pp. 245-247, 2006.
8. V. A. Kuznetsov, O. V. Senko, L. D. Miller, and A. V. Ivshina, "Statistically weighted voting analysis of microarrays for molecular pattern selection and discovery cancer genotypes," Int. J. Comput. Sci. Network Security, vol. 6, no. 12, pp. 73-83, 2006.
9. P. Broet, V. A. Kuznetsov, J. Bergh, E. T. Liu, and L. D. Miller, "Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients," Bioinformatics, vol. 22, no. 12, pp. 3288-3296, 2006.
10. R. D. Cox and D. Oakes, Analysis of Survival Data. London, U.K.: Chapman & Hall, 1984.
11. J. Okyere, S. T. May, M. van Zanten, L. A. C. J. Voesenek, and A. J. M. Peters, "How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results," BMC Bioinformatics, vol. 7, no. 137, 2006.
12. E. Motakis, G. P. Nason, P. Fryzlewicz, and G. A. Rutter, "Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach," Bioinformatics, vol. 22, no. 20, pp. 2547-2553, 2006.
13. N. E. Breslow, "Covariance analysis of censored survival data," Biometrics, vol. 30, no. 1, pp. 89-99, 1974.
14. T. M. Loughin, "A residual bootstrap for regression parameters in proportional hazards model," J. Stat. Comput. Simul., vol. 52, no. 4, pp. 367-384, 1995.
15. D. R. Cox and E. J. Snell, "A general definition of residuals (with discussion)," J. Roy. Stat. Soc. B, vol. 30, no. 3, pp. 248-265, 1968.
16. B. Efron and R. J. Tibshirani, An Introduction to the Bootstrap. New York: Chapman & Hall, 1994.
17. V. A. Kuznetsov, A. V. Ivshina, O. V. Senko, and A. V. Kuznetsova, "Syndrome approach for computer recognition of fuzzy systems and its application to immunological diagnostics and prognosis of human cancer," Math. Comput. Model., vol. 23, no. 6, pp. 92-112, 1996.
18. E. L. Kaplan and P. Meier, "Nonparametric estimation from incomplete observations," J. Amer. Stat. Assoc., vol. 53, no. 282, pp. 457-448, 1958.
19. A. Husdal, G. Bukholm, and I. R. Bukholm, "The prognostic value and overexpression of cyclin A is correlated with gene amplification of both cyclin A and cyclin E in breast cancer patient," Cell Oncol., vol. 28, no. 3, pp. 107-116, 2006.
20. X. Zhang, A. Guo, J. Yu, A. Possemato, Y. Chen, W. Zheng, R. D. Polakiewicz, K. W. Kinzler, B. Vogelstein, V. E. Velculescu, and Z. J. Wang, "Identification of STAT3 as a substrate of receptor protein tyrosine phosphatase T," Proc. Nat. Acad. Sci. USA, vol. 104, no. 10, pp. 4060-4064, 2007.
21. M. J. Rowling, C. M. Kemmis, D. A. Taffany, and J. Welsh, "Megalin-mediated endocytosis of vitamin D binding protein correlates with 25-hydroxycholecalciferol actions in human mammary cells," J. Nutr., vol. 136, no. 11, pp. 2754-2759, 2006.
22. J. Lin, J. E. Manson, I.-M. Lee, N. R. Cook, J. E. Buring, and S. M. Zhang, "Intakes of calcium and vitamin D and breast cancer risk in women," Arch. Intern. Med., vol. 167, no. 10, pp. 1050-1059, 2007.
23. T. Chiba, O. Yokosuka, K. Fukai, H. Kojima, M. Tada, M. Arai, F. Imazeki, and H. Saisho, "Cell growth inhibition and gene expression induced by the histone deacetylase inhibitor, trichostatin A, on human hepatoma cells," Oncology, vol. 66, no. 6, pp. 481-491, 2004.