Advanced Search
MyIDEAS: Login to save this article or follow this journal

Generalizing Moving Averages for Tiling Arrays Using Combined P-Value Statistics

Contents:

Author Info

  • Kechris Katerina J

    (University of Colorado Denver)

  • Biehs Brian

    (University of California, San Francisco)

  • Kornberg Thomas B

    (University of California, San Francisco)

Registered author(s):

    Abstract

    High density tiling arrays are an effective strategy for genome-wide identification of transcription factor binding regions. Sliding window methods that calculate moving averages of log ratios or t-statistics have been useful for the analysis of tiling array data. Here, we present a method that generalizes the moving average approach to evaluate sliding windows of p-values by using combined p-value statistics. In particular, the combined p-value framework can be useful in situations when taking averages of the corresponding test-statistic for the hypothesis may not be appropriate or when it is difficult to assess the significance of these averages. We exhibit the strengths of the combined p-values methods on Drosophila tiling array data and assess their ability to predict genomic regions enriched for transcription factor binding. The predictions are evaluated based on their proximity to target genes and their enrichment of known transcription factor binding sites. We also present an application for the generalization of the moving average based on integrating two different tiling array experiments.

    Download Info

    If you experience problems downloading a file, check if you have the proper application to view it first. In case of further problems read the IDEAS help page. Note that these files are not on the IDEAS site. Please be patient as the files may be large.
    File URL: http://www.degruyter.com/view/j/sagmb.2010.9.1/sagmb.2010.9.1.1434/sagmb.2010.9.1.1434.xml?format=INT
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.

    As the access to this document is restricted, you may want to look for a different version under "Related research" (further below) or search for a different version of it.

    Bibliographic Info

    Article provided by De Gruyter in its journal Statistical Applications in Genetics and Molecular Biology.

    Volume (Year): 9 (2010)
    Issue (Month): 1 (August)
    Pages: 1-31

    as in new window
    Handle: RePEc:bpj:sagmbi:v:9:y:2010:i:1:n:29

    Contact details of provider:
    Web page: http://www.degruyter.com

    Order Information:
    Web: http://www.degruyter.com/view/j/sagmb

    Related research

    Keywords:

    References

    No references listed on IDEAS
    You can help add them by filling out this form.

    Citations

    Lists

    This item is not listed on Wikipedia, on a reading list or among the top items on IDEAS.

    Statistics

    Access and download statistics

    Corrections

    When requesting a correction, please mention this item's handle: RePEc:bpj:sagmbi:v:9:y:2010:i:1:n:29. See general information about how to correct material in RePEc.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: (Peter Golla).

    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 references are entirely missing, you can add them using this form.

    If the full references list an item that is present in RePEc, but the system did not link 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 profile, as there may be some citations waiting for confirmation.

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