IDEAS home Printed from https://ideas.repec.org/a/eee/csdana/v56y2012i9p2718-2728.html
   My bibliography  Save this article

Identification of breast cancer prognosis markers via integrative analysis

Author

Listed:
  • Ma, Shuangge
  • Dai, Ying
  • Huang, Jian
  • Xie, Yang

Abstract

In breast cancer research, it is of great interest to identify genomic markers associated with prognosis. Multiple gene profiling studies have been conducted for such a purpose. Genomic markers identified from the analysis of single datasets often do not have satisfactory reproducibility. Among the multiple possible reasons, the most important one is the small sample sizes of individual studies. A cost-effective solution is to pool data from multiple comparable studies and conduct integrative analysis. In this study, we collect four breast cancer prognosis studies with gene expression measurements. We describe the relationship between prognosis and gene expressions using the accelerated failure time (AFT) models. We adopt a 2-norm group bridge penalization approach for marker identification. This integrative analysis approach can effectively identify markers with consistent effects across multiple datasets and naturally accommodate the heterogeneity among studies. Statistical and simulation studies demonstrate satisfactory performance of this approach. Breast cancer prognosis markers identified using this approach have sound biological implications and satisfactory prediction performance.

Suggested Citation

  • Ma, Shuangge & Dai, Ying & Huang, Jian & Xie, Yang, 2012. "Identification of breast cancer prognosis markers via integrative analysis," Computational Statistics & Data Analysis, Elsevier, vol. 56(9), pages 2718-2728.
    • Handle: RePEc:eee:csdana:v:56:y:2012:i:9:p:2718-2728
    DOI: 10.1016/j.csda.2012.02.017
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0167947312000990
    Download Restriction: Full text for ScienceDirect subscribers only.
    File URL: https://libkey.io/10.1016/j.csda.2012.02.017?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Lukas Meier & Sara Van De Geer & Peter Bühlmann, 2008. "The group lasso for logistic regression," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 70(1), pages 53-71, February.
    2. Stute, W., 1993. "Consistent Estimation Under Random Censorship When Covariables Are Present," Journal of Multivariate Analysis, Elsevier, vol. 45(1), pages 89-103, April.
    3. Susmita Datta & Jennifer Le-Rademacher & Somnath Datta, 2007. "Predicting Patient Survival from Microarray Data by Accelerated Failure Time Modeling Using Partial Least Squares and LASSO," Biometrics, The International Biometric Society, vol. 63(1), pages 259-271, March.
    4. Laura J. van 't Veer & Hongyue Dai & Marc J. van de Vijver & Yudong D. He & Augustinus A. M. Hart & Mao Mao & Hans L. Peterse & Karin van der Kooy & Matthew J. Marton & Anke T. Witteveen & George J. S, 2002. "Gene expression profiling predicts clinical outcome of breast cancer," Nature, Nature, vol. 415(6871), pages 530-536, January.
    5. Jian Huang & Shuange Ma & Huiliang Xie & Cun-Hui Zhang, 2009. "A group bridge approach for variable selection," Biometrika, Biometrika Trust, vol. 96(2), pages 339-355.
    6. Jian Huang & Shuangge Ma & Huiliang Xie, 2006. "Regularized Estimation in the Accelerated Failure Time Model with High-Dimensional Covariates," Biometrics, The International Biometric Society, vol. 62(3), pages 813-820, September.
    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. Khan Md Hasinur Rahaman & Bhadra Anamika & Howlader Tamanna, 2019. "Stability selection for lasso, ridge and elastic net implemented with AFT models," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 18(5), pages 1-14, October.
    2. Zhihua Sun & Yi Liu & Kani Chen & Gang Li, 2022. "Broken adaptive ridge regression for right-censored survival data," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 74(1), pages 69-91, February.
    3. Wang Zhu & Wang C.Y., 2010. "Buckley-James Boosting for Survival Analysis with High-Dimensional Biomarker Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-33, June.
    4. Yang, Yuan & McMahan, Christopher S. & Wang, Yu-Bo & Ouyang, Yuyuan, 2024. "Estimation of l0 norm penalized models: A statistical treatment," Computational Statistics & Data Analysis, Elsevier, vol. 192(C).
    5. Bilin Zeng & Xuerong Meggie Wen & Lixing Zhu, 2017. "A link-free sparse group variable selection method for single-index model," Journal of Applied Statistics, Taylor & Francis Journals, vol. 44(13), pages 2388-2400, October.
    6. Ruoqing Zhu & Ying-Qi Zhao & Guanhua Chen & Shuangge Ma & Hongyu Zhao, 2017. "Greedy outcome weighted tree learning of optimal personalized treatment rules," Biometrics, The International Biometric Society, vol. 73(2), pages 391-400, June.
    7. Pei Wang & Shunjie Chen & Sijia Yang, 2022. "Recent Advances on Penalized Regression Models for Biological Data," Mathematics, MDPI, vol. 10(19), pages 1-24, October.
    8. Xiaochao Xia & Binyan Jiang & Jialiang Li & Wenyang Zhang, 2016. "Low-dimensional confounder adjustment and high-dimensional penalized estimation for survival analysis," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 22(4), pages 547-569, October.
    9. T. Cai & J. Huang & L. Tian, 2009. "Regularized Estimation for the Accelerated Failure Time Model," Biometrics, The International Biometric Society, vol. 65(2), pages 394-404, June.
    10. Xianwen Ding & Zhihuang Yang, 2024. "Adaptive Bi-Level Variable Selection for Quantile Regression Models with a Diverging Number of Covariates," Mathematics, MDPI, vol. 12(20), pages 1-23, October.
    11. Yanfang Zhang & Chuanhua Wei & Xiaolin Liu, 2022. "Group Logistic Regression Models with l p,q Regularization," Mathematics, MDPI, vol. 10(13), pages 1-15, June.
    12. Hu, Jianwei & Chai, Hao, 2013. "Adjusted regularized estimation in the accelerated failure time model with high dimensional covariates," Journal of Multivariate Analysis, Elsevier, vol. 122(C), pages 96-114.
    13. Dong, Yan & Li, Daoji & Zheng, Zemin & Zhou, Jia, 2022. "Reproducible feature selection in high-dimensional accelerated failure time models," Statistics & Probability Letters, Elsevier, vol. 181(C).
    14. Mingqiu Wang & Guo-Liang Tian, 2019. "Adaptive group Lasso for high-dimensional generalized linear models," Statistical Papers, Springer, vol. 60(5), pages 1469-1486, October.
    15. Engler David & Li Yi, 2009. "Survival Analysis with High-Dimensional Covariates: An Application in Microarray Studies," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-24, February.
    16. Kaida Cai & Hua Shen & Xuewen Lu, 2022. "Adaptive bi-level variable selection for multivariate failure time model with a diverging number of covariates," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 31(4), pages 968-993, December.
    17. Wenjing Yin & Sihai Dave Zhao & Feng Liang, 2022. "Bayesian penalized Buckley-James method for high dimensional bivariate censored regression models," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 28(2), pages 282-318, April.
    18. Young Joo Yoon & Cheolwoo Park & Erik Hofmeister & Sangwook Kang, 2012. "Group variable selection in cardiopulmonary cerebral resuscitation data for veterinary patients," Journal of Applied Statistics, Taylor & Francis Journals, vol. 39(7), pages 1605-1621, January.
    19. Wenying Wu & Dingtao Peng, 2021. "Optimality Conditions for Group Sparse Constrained Optimization Problems," Mathematics, MDPI, vol. 9(1), pages 1-17, January.
    20. Haixiang Zhang & Jian Huang & Liuquan Sun, 2022. "Projection‐based and cross‐validated estimation in high‐dimensional Cox model," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 49(1), pages 353-372, March.

    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:eee:csdana:v:56:y:2012:i:9:p:2718-2728. 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: Catherine Liu (email available below). General contact details of provider: http://www.elsevier.com/locate/csda .

    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.