IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v12y2013i2p189-205n1003.html
   My bibliography  Save this article

Detection of epigenetic changes using ANOVA with spatially varying coefficients

Author

Listed:
  • Guanghua Xiao

    (Division of Biostatistics, Department of Clinical Sciences, The University of Texas Southwestern Medical Center at Dallas, TX 75390, USA)

  • Xinlei Wang

    (Department of Statistical Science, Southern Methodist University, Dallas, TX 75275, USA)

  • Quincey LaPlant

    (Fishberg Department of Neuroscience, Mount Sinai School of Medicine, New York, NY 10029, USA)

  • Nestler Eric J.

    (Fishberg Department of Neuroscience, Mount Sinai School of Medicine, New York, NY 10029, USA)

  • Xie Yang

    (Division of Biostatistics, Department of Clinical Sciences, The University of Texas Southwestern Medical Center at Dallas, TX 75390, USA)

Abstract

Identification of genome-wide epigenetic changes, the stable changes in gene function without a change in DNA sequence, under various conditions plays an important role in biomedical research. High-throughput epigenetic experiments are useful tools to measure genome-wide epigenetic changes, but the measured intensity levels from these high-resolution genome-wide epigenetic profiling data are often spatially correlated with high noise levels. In addition, it is challenging to detect genome-wide epigenetic changes across multiple conditions, so efficient statistical methodology development is needed for this purpose. In this study, we consider ANOVA models with spatially varying coefficients, combined with a hierarchical Bayesian approach, to explicitly model spatial correlation caused by location-dependent biological effects (i.e., epigenetic changes) and borrow strength among neighboring probes to compare epigenetic changes across multiple conditions. Through simulation studies and applications in drug addiction and depression datasets, we find that our approach compares favorably with competing methods; it is more efficient in estimation and more effective in detecting epigenetic changes. In addition, it can provide biologically meaningful results.

Suggested Citation

  • Guanghua Xiao & Xinlei Wang & Quincey LaPlant & Nestler Eric J. & Xie Yang, 2013. "Detection of epigenetic changes using ANOVA with spatially varying coefficients," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 12(2), pages 189-205.
    • Handle: RePEc:bpj:sagmbi:v:12:y:2013:i:2:p:189-205:n:1003
    DOI: 10.1515/sagmb-2012-0057
    as

    Download full text from publisher

    File URL: https://doi.org/10.1515/sagmb-2012-0057
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.1515/sagmb-2012-0057?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.

    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:bpj:sagmbi:v:12:y:2013:i:2:p:189-205:n:1003. 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.

    We have no bibliographic references for this item. You can help adding them by using 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: Peter Golla (email available below). General contact details of provider: https://www.degruyter.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.