IDEAS home Printed from https://ideas.repec.org/p/bep/mchbio/1039.html
   My bibliography  Save this paper

Semiparametric methods for identification of tumor progression genes from microarray data

Author

Listed:
  • Debashis Ghosh

    (University of Michigan)

  • Arul Chinnaiyan

    (University of Michigan Pathology and Urology)

Abstract

The use of microarray data has become quite commonplace in medical and scientific experiments. We focus here on microarray data generated from cancer studies. It is potentially important for the discovery of biomarkers to identify genes whose expression levels correlate with tumor progression. In this article, we develop statistical procedures for the identification of such genes, which we term tumor progression genes. Two methods are considered in this paper. The first is use of a proportional odds procedure, combined with false discovery rate estimation techniques to adjust for the multiple testing problem. The second method is based on order-restricted estimation procedures. The proposed methods are applied to data from a prostate cancer study. In addition, their finite-sample properties are compared using simulated data.

Suggested Citation

  • Debashis Ghosh & Arul Chinnaiyan, 2004. "Semiparametric methods for identification of tumor progression genes from microarray data," The University of Michigan Department of Biostatistics Working Paper Series 1039, Berkeley Electronic Press.
    • Handle: RePEc:bep:mchbio:1039
    Note: oai:bepress.com:umichbiostat-1039
    as

    Download full text from publisher

    File URL: http://www.bepress.com/cgi/viewcontent.cgi?article=1039&context=umichbiostat
    Download Restriction: no
    ---><---

    References listed on IDEAS

    as
    1. L. Ferrante & S. Bompadre & L. Possati & L. Leone, 2000. "Parameter Estimation in a Gompertzian Stochastic Model for Tumor Growth," Biometrics, The International Biometric Society, vol. 56(4), pages 1076-1081, December.
    2. Saravana M. Dhanasekaran & Terrence R. Barrette & Debashis Ghosh & Rajal Shah & Sooryanarayana Varambally & Kotoku Kurachi & Kenneth J. Pienta & Mark A. Rubin & Arul M. Chinnaiyan, 2001. "Delineation of prognostic biomarkers in prostate cancer," Nature, Nature, vol. 412(6849), pages 822-826, August.
    3. John D. Storey, 2002. "A direct approach to false discovery rates," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 64(3), pages 479-498, August.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Debashis Ghosh & Arul Chinnaiyan, 2004. "Covariate adjustment in the analysis of microarray data from clinical studies," The University of Michigan Department of Biostatistics Working Paper Series 1030, Berkeley Electronic Press.
    2. Youngchao Ge & Sandrine Dudoit & Terence Speed, 2003. "Resampling-based multiple testing for microarray data analysis," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 12(1), pages 1-77, June.
    3. Bajgrowicz, Pierre & Scaillet, Olivier, 2012. "Technical trading revisited: False discoveries, persistence tests, and transaction costs," Journal of Financial Economics, Elsevier, vol. 106(3), pages 473-491.
    4. Wen Shi & Xi Chen & Jennifer Shang, 2019. "An Efficient Morris Method-Based Framework for Simulation Factor Screening," INFORMS Journal on Computing, INFORMS, vol. 31(4), pages 745-770, October.
    5. Dørum Guro & Snipen Lars & Solheim Margrete & Saebo Solve, 2011. "Smoothing Gene Expression Data with Network Information Improves Consistency of Regulated Genes," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-26, August.
    6. Jianqing Fan & Xu Han, 2017. "Estimation of the false discovery proportion with unknown dependence," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 79(4), pages 1143-1164, September.
    7. A Bottle & P Aylin, 2011. "Predicting the false alarm rate in multi-institution mortality monitoring," Journal of the Operational Research Society, Palgrave Macmillan;The OR Society, vol. 62(9), pages 1711-1718, September.
    8. Van Hanh Nguyen & Catherine Matias, 2014. "On Efficient Estimators of the Proportion of True Null Hypotheses in a Multiple Testing Setup," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 41(4), pages 1167-1194, December.
    9. Shigeyuki Matsui & Hisashi Noma, 2011. "Estimating Effect Sizes of Differentially Expressed Genes for Power and Sample-Size Assessments in Microarray Experiments," Biometrics, The International Biometric Society, vol. 67(4), pages 1225-1235, December.
    10. Lianming Wang & David B. Dunson, 2010. "Semiparametric Bayes Multiple Testing: Applications to Tumor Data," Biometrics, The International Biometric Society, vol. 66(2), pages 493-501, June.
    11. Ebrahimi, Nader, 2008. "Simultaneous control of false positives and false negatives in multiple hypotheses testing," Journal of Multivariate Analysis, Elsevier, vol. 99(3), pages 437-450, March.
    12. B. Moerkerke & E. Goetghebeur & J. De Riek & I. Roldán‐Ruiz, 2006. "Significance and impotence: towards a balanced view of the null and the alternative hypotheses in marker selection for plant breeding," Journal of the Royal Statistical Society Series A, Royal Statistical Society, vol. 169(1), pages 61-79, January.
    13. Zaili Fang & Inyoung Kim & Jeesun Jung, 2018. "Semiparametric Kernel-Based Regression for Evaluating Interaction Between Pathway Effect and Covariate," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 23(1), pages 129-152, March.
    14. Mark Rempel, 2016. "Improving Overnight Loan Identification in Payments Systems," Journal of Money, Credit and Banking, Blackwell Publishing, vol. 48(2-3), pages 549-564, March.
    15. Timothy B. Armstrong, 2014. "Adaptive Testing on a Regression Function at a Point," Cowles Foundation Discussion Papers 1957R, Cowles Foundation for Research in Economics, Yale University, revised Feb 2015.
    16. Nucera, Federico & Valente, Giorgio, 2013. "Carry trades and the performance of currency hedge funds," Journal of International Money and Finance, Elsevier, vol. 33(C), pages 407-425.
    17. Axel Gandy & Georg Hahn, 2016. "A Framework for Monte Carlo based Multiple Testing," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 43(4), pages 1046-1063, December.
    18. Gutiérrez, R. & Nafidi, A. & Gutiérrez Sánchez, R., 2005. "Forecasting total natural-gas consumption in Spain by using the stochastic Gompertz innovation diffusion model," Applied Energy, Elsevier, vol. 80(2), pages 115-124, February.
    19. Sinha, Sanjoy K. & Kaushal, Amit & Xiao, Wenzhong, 2014. "Inference for longitudinal data with nonignorable nonmonotone missing responses," Computational Statistics & Data Analysis, Elsevier, vol. 72(C), pages 77-91.
    20. Iain Melvin & Jason Weston & William Stafford Noble & Christina Leslie, 2011. "Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding," PLOS Computational Biology, Public Library of Science, vol. 7(1), pages 1-8, January.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:bep:mchbio:1039. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Christopher F. Baum (email available below). General contact details of provider: http://www.bepress.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.