Robust likelihood-based survival modeling with microarray data

Journal of Statistical Software

Volumn 29, Issue 1, 2009, Pages

  Cho, Hyung Jun ^a   Yu, Ami ^a   Kim, Sukwoo ^a   Kang, Jaewoo ^a   Hong, Seung Mo ^b  

^a Korea University   (South Korea)

^b DEPARTMENT OF PATHOLOGY   (United States)

Author keywords

Likelihood; Microarray data; R; Robustness; Survival data

Indexed keywords

EID: 58449134524     PISSN: 15487660     EISSN: 15487660     Source Type: Journal    
DOI: 10.18637/jss.v029.i01     Document Type: Article

References (29)

1. Bair E, Tibshirani R (2004). "Semi-Supervised Methods to Predict Patient Survival from Gene Expression Data." PLoS Biology, 2, 0511-0521.
2. Beer DG, Kardia SL, Huang CC, Giordano TJ, Levin AM, Misek DE, Lin L, Chen G, Gharib TG, Thomas DG, Lizyness ML, Kuick R, Hayasaka S, Taylor JM, Iannettoni MD, Orringer MB, Hanash S (2002). "Gene-Expression Profiles Predict Survival of Patients with Lung Adenocarcinoma." Nature Medicine, 8, 816-824.
3. Cox DR (1972). "Regression Models and Life Tables." Journal of the Royal Statistical Society B, 34, 187-220.
4. Ein-Dor L, Kela I, Getz G, Givol D, E D (2005). "Outcome Signature Genes in Breast Cancer: Is There a Unique Set?" Bioinformatics, 21, 171-178.
5. Freije WA, Castro-Vargas FE, Fang Z, Horvath S, Cloughesy T, Liau LM, Mischel PS, Nelson SF (2004). "Gene Expression Profiling of Gliomas Strongly Predicts Survival." Cancer Research, 64, 6503-6510.
6. Gary SC, Zerillo CA, Chiang VL, Gaw JU, Gray G, Hockfield S (2000). "cDNA Cloning, Chromosomal Localization, and Expression Analysis of Human BEHAB/Brevican, a Brain Specific Proteoglycan Regulated during Cortical Development and in Glioma." Gene, 256, 139-147.
7. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisen F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: Open Software Development for Computational Biology and Bioinformatics." Genome Biology, 5, R80. URL http://genomebiology.com/2004/5/10/R80.
8. Goeman JJ, Oosting J, Cleton-Jansen AM, Anninga JK, van Houwelingen HC (2005). "Testing Association of a Pathway with Survival Using Gene Expression Data." Bioinformatics, 21, 1950-1957.
9. Gui J, Li H (2005). "Penalized Cox Regression Analysis in the High-dimensional and Low-sample Size Settings, with Applications to Microarray Gene Expression Data." Bioinformatics, 21, 3001-3008.
10. Held-Feindt J, Paredes EB, Blomer U, Seidenbecher C, Stark AM, Mehdorn HM, R M (2006). "Matrix-Degrading Proteases ADAMTS4 and ADAMTS5 (Disintegrins and Metalloproteinases with Thrombospondin Motifs 4 and 5) Are Expressed in Human Glioblastomas." International Journal of Cancer, 118, 55-61.
11. Jaworski DM, Kelly GM, Piepmeier JM, S H (1996). "BEHAB (Brain Enriched Hyaluronan Binding) Is Expressed in Surgical Samples of Glioma and in Intracranial Grafts of Invasive Glioma Cell Lines." Cancer Research, 56, 2293-2298.
12. Jenssen TK, Kuo WP, Stokke T, E H (2002). "Associations between Gene Expressions in Breast Cancer and Patient Survival." Human Genetics, 111, 411-420.
13. Jung SH, Owzar K, George SL (2005). "A Multiple Testing Procedure to Associate Gene Expression Levels with Survival." Statistics in Medicine, 24, 3077-2088.
14. Mandruzzato S, Callegaro A, Turcatel G, Francescato S, Montesco MC, Chiarion-Sileni V, Mocellin S, Rossi CR, Bicciato S, Wang E, Marincola FM, Zanovello P (2006). "A Gene Expression Signature Associated with Survival in Metastatic Melanoma." Journal of Translational Medicine, 4, 50.
15. Matsui S (2006). "Predicting Survival Outcomes Using Subsets of Significant Genes in Prognostic Marker Studies with Microarrays." BMC Bioinformatics, 7, 156.
16. Nakada M, Miyamori H, Kita D, Takahashi T, Yamashita J, Sato H, Miura R, Yamaguchi Y, Okada Y (2005). "Human Glioblastomas Overexpress ADAMTS-5 that Degrades Brevican." Acta Neuropathologica, 110, 239-246.
17. Nguyen DV, Rocke DM (2002). "Partial Least Squares Proportional Hazard Regression for Application to DNA Microarray Survival Data." Bioinformatics, 18, 1625-32.
18. Nutt CL, Zerillo CA, Kelly GM, Hockfield S (2001). "Brain Enriched Hyaluronan Binding (BEHAB)/Brevican Increases Aggressiveness of CNS-1 Gliomas in Lewis Rats." Cancer Research, 61, 7056-7059.
19. Park PJ, Tian L, Kohane IS (2002). "Linking Gene Expression Data with Patient Survival Times Using Partial Least Squares." Bioinformatics, 18 Suppl 1, S120-S127.
20. R Development Core Team (2008). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/.
21. Rosenwald A, Wright G, Chan WC, Connors JM, Campo E, Fisher RI, Gascoyne RD, Muller-Hermelink HK, Smeland EB, Giltnane JM, Hurt EM, Zhao H, Averett L, Yang L, Wilson WH, Jaffe ES, Simon R, Klausner RD, Powell J, Duffey PL, Longo DL, Greiner TC, Weisenburger DD, Sanger WG, Dave BJ, Lynch JC, Vose J, Armitage JO, Montserrat E, Lopez-Guillermo A, Grogan TM, Miller TP, LeBlanc M, Ott G, Kvaloy S, Delabie J, Holte H, Krajci P, Stokke T, Staudt LM (2002). "The Use of Molecular Profiling to Predict Survival after Chemotherapy for Diffuse Large-B-Cell Lymphoma." The New England Journal of Medicine, 346, 1937-1947.
22. Sanchez-Carbayo M, Socci ND, Lozano J, Saint F, Cordon-Cardo C (2006). "Defining Molecular Profiles of Poor Outcome in Patients with Invasive Bladder Cancer Using Oligonucleotide Microarrays." Journal of Clinical Oncology, 24, 778-789.
23. Sha N, Tadesse MG, Vannucci M (2006). "Bayesian Variable Selection for the Analysis of Microarray Data with Censored Outcomes." Bioinformatics, 22, 2262-2268.
24. Shannon WD, Watson MA, Perry A, Rich K (2002). "Mantel Statistics to Correlate Gene Expression Levels from Microarrays with Clinical Covariates." Genetic Epidemiology, 23, 87-96.
25. Tadesse MG, Ibrahim JG, Gentleman R, Chiaretti S, Ritz J, Foa R (2005). "Bayesian Error-in-Variable Survival Model for the Analysis of GeneChip Arrays." Biometrics, 61, 488-497.
26. Therneau T, Lumley T (2008). survival: Survival Analysis Including Penalised Likelihood. R package version 2.34-1, URL http://CRAN.R-project.org/package=survival.
27. Wigle DA, Jurisica I, Radulovich N, Pintilie M, Rossant J, Liu N, Lu C, Woodgett J, Seiden I, Johnston M, Keshavjee S, Darling G, Winton T, Breitkreutz BJ, Jorgenson P, Tyers M, Shepherd FA, Tsao MS (2002). "Molecular Profiling of Non-Small Cell Lung Cancer and Correlation with Disease-Free Survival." Cancer Research, 62, 3005-3008.
28. Xu J, Yang Y, Ott J (2005). "Survival Analysis of Microarray Expression Data by Transformation Models." Computational Biology and Chemistry, 29, 91-94.
29. Yamaguchi Y (2000). "Lecticans: Organizers of the Brain Extracellular Matrix." Cellular and Molecular Life Sciences, 57, 276-289.