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Original Articles

A Predictive Risk Probability Approach for Microarray Data with Survival as an Endpoint

, , , , &
Pages 841-852 | Received 21 Aug 2007, Accepted 05 Feb 2008, Published online: 10 Sep 2008

REFERENCES

  • Bair , E. , Tibshirani , R. ( 2004 ). Semi-supervised methods to predict patient survival from gene expression data . PLoS Biol. 2 : E108 .
  • Benjamini , Y. , Hochberg , Y. ( 1995 ). Controlling the false discovery rate: A practical and powerful approach to multiple testing . J. R. Stat. Soc. Ser. B Methodological 57 : 289 – 300 .
  • Eschrich , S. , Yang , I. , Bloom , G. , Kwong , K. Y. , Boulware , D. , Cantor , A. , Coppola , D. , Kruhoffer , M. , Aaltonen , L. , Orntoft , T. F. , Quackenbush , J. , Yeatman , T. J. ( 2005 ). Molecular staging for survival prediction of colorectal cancer patients . J. Clin. Oncol. 23 : 3526 – 3535 .
  • Fan , R. , Chen , P. H. , Lin , C. ( 2005 ). Working set selection using the second order information for training SVM . Journal of Machine Learning Research 6 : 1889 – 1918 .
  • Hastie , T. J. , Pregibon , D. ( 1992 ). Chapter 6: Generalized linear models . In: Chambers , J. M. , Hastie , T. J. , eds. Statistical Models in S . Wadsworth & Brooks/Cole .
  • Huang , E. S. , Black , E. P. , Dressman , H. , West , M. , Nevins , J. R. ( 2003 ). Gene expression phenotypes of oncogenic signaling pathways . Cell Cycle 2 : 415 – 417 .
  • Irizarry , R. A. , Bolstad , B. M. , Collin , F. , Cope , L. M. , Hobbs , B. , Speed , T. P. ( 2003 ). Summaries of Affymetrix GeneChip probe level data . Nucleic Acids Res. 31 : e15 .
  • Nguyen , D. V. , Rocke , D. M. ( 2002 ). Partial least squares proportional hazard regression for application to DNA microarray survival data . Bioinformatics 18 : 1625 – 1632 .
  • Park , P. J. , Tian , L. , Kohane , I. S. ( 2002 ). Linking gene expression data with patient survival times using partial least squares . Bioinformatics 18 ( Suppl. 1 ): S120 – S127 .
  • Rosenwald , A. , Wright , G. , Chan , W. C. , Connors , J. M. , Campo , E. , Fisher , R. I. , Gascoyne , R. D. , Muller-Hermelink , H. K. , Smeland , E. B. , Giltnane , J. M. , Hurt , E. M. , Zhao , H. , Averett , L. , Yang , L. , Wilson , W. H. , Jaffe , E. S. , Simon , R. , Klausner , R. D. , Powell , J. , Duffey , P. L. , Longo , D. L. , Greiner , T. C. , Weisenburger , D. D. , Sanger , W. G. , Dave , B. J. , Lynch , J. C. , Vose , J. , Armitage , J. O. , Montserrat , E. , Lopez-Guillermo , A. , Grogan , T. M. , Miller , T. P. , LeBlanc , M. , Ott , G. , Kvaloy , S. , Delabie , J. , Holte , H. , Krajci , P. , Stokke , T. , Staudt , L. M. ( 2002 ). The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma . N. Engl. J. Med. 346 : 1937 – 1947 .
  • Sorlie , T. , Tibshirani , R. , Parker , J. , Hastie , T. , Marron , J. S. , Nobel , A. , Deng , S. , Johnsen , H. , Pesich , R. , Geisler , S. , Demeter , J. , Perou , C. M. , Lonning , P. E. , Brown , P. O. , Borresen-Dale , A. L. , Botstein , D. ( 2003 ). Repeated observation of breast tumor subtypes in independent gene expression data sets . Proc. Natl. Acad. Sci. USA 100 : 8418 – 8423 .
  • Therneau , T. M. , Atkinson , B. ( 2006 ). rpart: Recursive Partitioning . R Package ( Software package ).
  • Tusher , V. G. , Tibshirani , R. , Chu , G. ( 2001 ). Significance analysis of microarrays applied to the ionizing radiation response . Proc. Natl. Acad. Sci. USA 98 : 5116 – 5121 .
  • van't Veer , L. J. , Paik , S. , Hayes , D. F. ( 2005 ). Gene expression profiling of breast cancer: a new tumor marker . J. Clin. Oncol. 23 : 1631 – 1635 .
  • van de Vijver , M. J. , He , Y. D. , van't Veer , L. J. , Dai , H. , Hart , A. A. , Voskuil , D. W. , Schreiber , G. J. , Peterse , J. L. , Roberts , C. , Marton , M. J. , Parrish , M. , Atsma , D. , Witteveen , A. , Glas , A. , Delahaye , L. , van der Velde , T. , Bartelink , H. , Rodenhuis , S. , Rutgers , E. T. , Friend , S. H. , Bernards , R. ( 2002 ). A gene-expression signature as a predictor of survival in breast cancer . N. Engl. J. Med. 347 : 1999 – 2009 .
  • Venables , W. N. , Ripley , B. D. ( 2002 ). Modern Applied Statistics with S. , 4th ed. New York : Springer .
  • West , M. , Blanchette , C. , Dressman , H. , Huang , E. , Ishida , S. , Spang , R. , Zuzan , H. , Olson Jr. , J. A. , Marks , J. R. , Nevins , J. R. ( 2001 ). Predicting the clinical status of human breast cancer by using gene expression profiles . Proc. Natl. Acad. Sci.USA 98 : 11462 – 11467 .

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