Partial least squares proportional hazard regression for application to DNA microarray survival data

Bioinformatics

Volumn 18, Issue 12, 2002, Pages 1625-1632

  Nguyen, Danh V ^a   Rocke, David M ^b  

^a TEXAS A AND M UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ADVANCED CANCER; ARTICLE; B CELL LYMPHOMA; BREAST CARCINOMA; CANCER RESEARCH; CANCER SURVIVAL; CONTROLLED STUDY; DNA MICROARRAY; EXPRESSION VECTOR; GENE EXPRESSION; GENETIC TRANSCRIPTION; HUMAN; HUMAN TISSUE; MATHEMATICAL COMPUTING; METHODOLOGY; NONBIOLOGICAL MODEL; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROSPECTIVE STUDY; REGRESSION ANALYSIS; VALIDATION PROCESS;

VECTORS;

EID: 0036956225     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.12.1625     Document Type: Article

References (24)

1. Alizadeh,A.A., Eisen,M.B., Davis,R.E., Ma,C., Lossos,I.S., Rosenwald,A., Broldrick,J.C., Sabet,H., Tran,T., Yu,X. et al. (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, 403, 503-511.
2. Arjas,E. (1988) A graphical method for assessing goodness-of-fit in Cox's proportional hazards models. J. Am. Stat. Assoc., 83, 204-212.
3. Breslow,N. (1975) Analysis of survival data under the proportional hazard model. Int. Statist. Rev., 43, 45-57.
4. Cox,D.R. (1972) Regression models and life-tables (with discussion). J. R. Stat. Soc., B 34, 187-220.
5. Cox,D.R. (1975) Partial likelihood. Biometrika, 62, 269-276.
6. DeRisi,J., Penland,L., Brown,P.O., Bittner,M.L., Meltzer,P.S., Ray,M., Chen,Y., Su,Y.A. and Trent,J.M. (1996) Use of cDNA microarray to analyse gene expression patterns in human cancer. Nature Genet., 14, 457-460.
7. Frank,I.E. and Friedman,J.H. (1993) A statistical view of some chemometrics regression tools (with discussion). Technometrics, 35, 109-148.
8. Grambsch,P. and Therneau,T.M. (1994) Proportional harzards tests and diagnostics based on weighted residuals. Biometrika, 81, 515-526.
9. Helland,I.S. (1988) On the structure of partial least squares. Commun. Stat.-Simul. Comput., 17, 581-607.
10. Höskuldsson,A. (1988) PLS regression methods. J. Chem., 2, 211-228.
11. Kalbfleisch,J.D. and Prentice,R.L. (1973) Marginal likelihoods based on Cox's regression and like model. Biometrika, 60, 267-278.
12. Kaplan.E.L. and Meier,P. (1958) Nonparametric estimation from incomplete observations. J. Am. Stat. Assoc., 53, 457-481.
13. Lockhart,D.J., Dong,H., Byrne,M.C., Follettie,M.T., Gallo,M.V., Chee,M.S., Mittermann,M., Wang,C., Kobayashi,M., Horton,H. and Brown,E.L. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol., 14, 1675-1680.
14. Martens,H. and Naes,T. (1989) Multivariate Calibration. Wiley, New York.
15. Nguyen,D.V. and Rocke,D.M. (2002) Classification of acute leukemia based on DNA microarray gene expressions using partial least squares. In Lin,S.M and Johnson,K.F. (eds), Methods of Microarray Data Analysis. Kluwer, Dordrecht, pp. 109-124.
16. Nguyen,D.V. and Rocke,D.M. (2002b) Tumor classification by partial least squares using gene expression data. Bioinformatics, 18, 39-50.
17. Nguyen,D.V. and Rocke,D.M. (2002c) Multi-class cancer classification via partial least squares with gene expression profiles. Bioinformatics, 18, 1216-1226.
18. Perou,C.M., Sorlie,T., Eisen,M.B., van de Rijn,M., Jeffrey,S.S., Rees,C.A., Pollack,J.R., Ross,D.T., Johnsen,H., Akslen,L.A., Fluge,O. et al. (2000) Molecular portrait of human breast tumors. Nature, 406, 747-752.
19. Ross,D.T., Scherf,U., Eisen,M.B., Perou,C.M., Rees,C., Spellman,P., Iyer,V., Jeffrey,S.S., Rijin,M.V., Waltham,M. et al. (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat. Genet., 24, 227-235.
20. Schemper,M. (1992) Further results on the explained variation in proportional hazards regression. Biometrika, 79, 202-204.
21. Schena,M., Shalon,D., Davis,R.W. and Brown,P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467-470.
22. Schoenfeld,D. (1982) Chi-square goodness-of-fit tests for proportional hazards regression. Biometrika, 67, 145-153.
23. Sørlie,T., Perou,C.M., Tibshirani,R., Aas,T., Geisler,S., Johnsen,H., Hastie,T., Eisen,M.B., van de Rijn,M., Jeffrey,S.S. et al. (2001) Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl Acad. Sci. USA, 98, 10869-10874.
24. Wold,S. (1994) PLS for Multivariate Linear Modeling. In van de Vaterbeemd,H. (ed.), Chemometric Methods in Molecular Design. Verlag-Chemie, Weinheim, pp. 195-218.