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Two-Way Horizontal and Vertical Omics Integration for Disease Subtype Discovery

Author

Listed:
  • Zhiguang Huo

    (University of Florida)

  • Li Zhu

    (University of Pittsburgh)

  • Tianzhou Ma

    (University of Maryland)

  • Hongcheng Liu

    (University of Florida)

  • Song Han

    (University of Florida)

  • Daiqing Liao

    (University of Florida)

  • Jinying Zhao

    (University of Florida)

  • George Tseng

    (University of Pittsburgh)

Abstract

Disease subtype discovery is an essential step in delivering personalized medicine. Disease subtyping via omics data has become a common approach for this purpose. With the advancement of technology and the lower price for generating omics data, multi-level and multi-cohort omics data are prevalent in the public domain, providing unprecedented opportunities to decrypt disease mechanisms. How to fully utilize multi-level/multi-cohort omics data and incorporate established biological knowledge toward disease subtyping remains a challenging problem. In this paper, we propose a meta-analytic integrative sparse Kmeans (MISKmeans) algorithm for integrating multi-cohort/multi-level omics data and prior biological knowledge. Compared with previous methods, MISKmeans shows better clustering accuracy and feature selection relevancy. An efficient R package, “MIS-Kmeans”, calling C++ is freely available on GitHub (https://github.com/Caleb-Huo/MIS-Kmeans).

Suggested Citation

  • Zhiguang Huo & Li Zhu & Tianzhou Ma & Hongcheng Liu & Song Han & Daiqing Liao & Jinying Zhao & George Tseng, 2020. "Two-Way Horizontal and Vertical Omics Integration for Disease Subtype Discovery," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 12(1), pages 1-22, April.
  • Handle: RePEc:spr:stabio:v:12:y:2020:i:1:d:10.1007_s12561-019-09242-6
    DOI: 10.1007/s12561-019-09242-6
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    References listed on IDEAS

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    1. Ronglai Shen & Qianxing Mo & Nikolaus Schultz & Venkatraman E Seshan & Adam B Olshen & Jason Huse & Marc Ladanyi & Chris Sander, 2012. "Integrative Subtype Discovery in Glioblastoma Using iCluster," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-9, April.
    2. Robert Tibshirani & Guenther Walther & Trevor Hastie, 2001. "Estimating the number of clusters in a data set via the gap statistic," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 63(2), pages 411-423.
    3. Zhiguang Huo & Ying Ding & Silvia Liu & Steffi Oesterreich & George Tseng, 2016. "Meta-Analytic Framework for Sparse K -Means to Identify Disease Subtypes in Multiple Transcriptomic Studies," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 111(513), pages 27-42, March.
    4. Glenn Milligan & Martha Cooper, 1985. "An examination of procedures for determining the number of clusters in a data set," Psychometrika, Springer;The Psychometric Society, vol. 50(2), pages 159-179, June.
    5. Charles M. Perou & Therese Sørlie & Michael B. Eisen & Matt van de Rijn & Stefanie S. Jeffrey & Christian A. Rees & Jonathan R. Pollack & Douglas T. Ross & Hilde Johnsen & Lars A. Akslen & Øystein Flu, 2000. "Molecular portraits of human breast tumours," Nature, Nature, vol. 406(6797), pages 747-752, August.
    6. Lawrence Hubert & Phipps Arabie, 1985. "Comparing partitions," Journal of Classification, Springer;The Classification Society, vol. 2(1), pages 193-218, December.
    7. Adaikalavan Ramasamy & Adrian Mondry & Chris C Holmes & Douglas G Altman, 2008. "Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets," PLOS Medicine, Public Library of Science, vol. 5(9), pages 1-13, September.
    8. Patrick Danaher & Pei Wang & Daniela M. Witten, 2014. "The joint graphical lasso for inverse covariance estimation across multiple classes," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 76(2), pages 373-397, March.
    9. Witten, Daniela M. & Tibshirani, Robert, 2010. "A Framework for Feature Selection in Clustering," Journal of the American Statistical Association, American Statistical Association, vol. 105(490), pages 713-726.
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