Development and validation of predictive indices for a continuous outcome using gene expression profiles

Cancer Informatics

Volumn 9, Issue , 2010, Pages 105-114

  Zhao, Yingdong ^a   Simon, Richard ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Continuous outcome; Gene expression; Regression model

Indexed keywords

PACLITAXEL;

ARTICLE; AVERAGED LINEAR REGRESSION ANALYSIS; CANCER INHIBITION; CYTOTOXICITY; GENE EXPRESSION PROFILING; GENETIC ALGORITHM; GLEASON SCORE; LEAST ABSOLUTE SHRINKAGE AND SELECTION OPERATOR; LEAST ANGLE REGRESSION ANALYSIS; LINEAR REGRESSION ANALYSIS; LUNG CANCER; MATHEMATICAL MODEL; MICROARRAY ANALYSIS; PREDICTION; PROSTATE CANCER; SIMULATION; VALIDATION PROCESS; ALGORITHM; HUMAN;

EID: 77952892427     PISSN: 11769351     EISSN: 11769351     Source Type: Journal    
DOI: 10.4137/cin.s3805     Document Type: Article

References (22)

1. Wang E, Miller LD, Ohnmacht GA, et al. Evolving molecular portraits of metastatic melanoma. Cancer Res. 2002;62:3581-6.
2. Radmacher MD, McShane LM, Simon RM. A paradigm for class prediction using gene expression profiles. J Comput Biol. 2002;9:505-11
3. Dudoit S, Fridlyand J, Speed TP. Comparison of discrimination methods for the classification of tumors using gene expression data. Journal of the American Statistical Association. 2002;97:77-87.
4. Fix E, Hodges JL. Discriminatory analysis, nonparametric discrimination: Consistency properties. Technical Report 4, USAF School of Aviation Medicine, Randolph Field, Texas; 1951.
5. Tibshirani R, et al. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A. 2002;99:6567-72
6. Furey TS, Cristianini N, Duffy N, Bednarski DW, Schummer M, Haussler D. Support vector machine classification and validation of cancer tissue sam- ples using microarray expression data. Bioinformatics. 2000;16:906-14
7. Zhang H, Yu CY, Singer B. Cell and tumor classification using gene expression data: construction of forest. Proc Natl Acad Sci U S A. 2003;100: 4168-72.
8. Simon R, Lam AP, Li MC, Ngan M, Menenzes S, Zhao Y. Analysis of Gene Expression Data Using BRB-ArrayTools. Cancer Informatics. 2007;2:1-7.
9. Molinaro A, Simon R, Pfeiffer R. Prediction error estimation: A comparison of resampling methods. Bioinformatics. 2005;21:3301-7.
10. Bovelstad HM, Nygard S, Storvold HL, et al. Predicting survival from microarray data-a comparative study. Bioinformatics. 2007;23:2080-7
11. Dupuy A, Simon RM. Critical review of published Microarray studies for cancer outcome and guidelines on statistical analysis and reporting. Journal of the National Cancer Institute. 2007;99:147-57.
12. Bibikova B, et al. Expression signatures that correlated with Gleason score and relapse in prostate cancer. Genomics. 2007;89:666-72.
13. Simon R, Radmacher M, Dobbin K, McShane, LM. Pitfalls in the Use of DNA Microarray Data for Diagnostic and Prognostic Classification. Journal of the National Cancer Institute. 2003;95:14-8.
14. Efron B, Hastie T, Johnstone I, Tibshirani R. Least Angle Regression. Annals of Statistics. 2004;32:407-99.
15. Tibshirani R. Regression shrinkage and selection via the lasso. J Royal Statist Soc B. 1996;58:267-88.
16. Hastie T, Tibshirani R, Friedman J. The Elements of Statistical Learning; Data mining, Inference and Prediction. Springer Verlag, New York; 2001.
17. Hesterberg T, Choi NH, Meier L, Fraley C. Least angle and ℓ1 penalized regression: A review. Statist Surv. 2008;2:61-93.
18. Tibshirani B, Hastie T, et al. Sample classification from protein mass spectrometry, by 'peak probability contrasts'. Bioinformatics. 2004;20: 3034-44.
19. Wu TT, Chen YF, Hastie T, Sobel E, Lange K. Genome-wide association analysis by lasso penalized logistic regression. Bioinformatics. 25: 714-21.
20. Beer, et al. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med. 2002;8:816-24.
21. Zhao Y, Simon R. BRB-ArrayTools Data Archive for Human Cancer Gene Expression: A Unique and Efficient Data Sharing Resource. Cancer Informatics. 2008;6:9-15.
22. Gemma A, Li C, Sugiyama Y, et al. Anticancer drug clustering in lung cancer based on gene expression profiles and sensitivity database. BMC Cancer. 2006;6:174-81.