IDEAS home Printed from https://ideas.repec.org/
MyIDEAS: Login to save this paper or follow this series

Over-represented sequences located on UTRs are potentially involved in regulatory functions

  • Kihoon Yoon

    (The University of Texas Health)

  • Daijin Ko

    (The University of Texas at San Antonio)

  • Carolina B. Livi

    (The University of Texas at San Antonio)

  • Nathan Trinklein

    (SwitchGear Genomics)

  • Mark Doderer

    (The University of Texas at San Antonio)

  • Stephen Kwek

    (The University of Texas at San Antonio)

  • Luiz O. F. Penalva

    (The University of Texas Health)

Registered author(s):

    Eukaryotic gene expression must be coordinated for the proper functioning of biological processes. This coordination can be achieved both at the transcriptional and post-transcriptional levels. In both cases, regulatory sequences placed at either promoter regions or on UTRs function as markers recognized by regulators that can then activate or repress different groups of genes according to necessity. While regulatory sequences involved in transcription are quite well documented, there is a lack of information on sequence elements involved in post-transcriptional regulation. We used a statistical over-representation method to identify novel regulatory elements located on UTRs. An exhaustive search approach was used to calculate the frequency of all possible n-mers (short nucleotide sequences) in 16,160 human genes of NCBI RefSeq sequences and to identify any peculiar usage of n-mers on UTRs. After a stringent filtering process, we identified circa 4,000 highly over-represented n-mers on UTRs. We provide evidence that these n-mers are potentially involved in regulatory functions. Identified n-mers overlap with previously identified binding sites for HuR and Tia1 and, AU-rich and GU-rich sequences. We determined also that over-represented n-mers are particularly enriched in a group of 159 genes directly involved in tumor formation. Finally, a method to cluster n-mer groups allowed the identification of putative gene networks.

    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://business.utsa.edu/wps/MSS/0053MSS-301-2008.pdf
    File Function: Full text
    Download Restriction: no

    Paper provided by College of Business, University of Texas at San Antonio in its series Working Papers with number 0053.

    as
    in new window

    Length: 39 pages
    Date of creation:
    Date of revision:
    Handle: RePEc:tsa:wpaper:0053
    Contact details of provider: Postal: 6900 North Loop 1604 West, San Antonio, TX 78249-0631
    Phone: 210.458.4313
    Fax: 210.458.4308
    Web page: http://business.utsa.edu/wps

    More information through EDIRC

    References listed on IDEAS
    Please report citation or reference errors to , or , if you are the registered author of the cited work, log in to your RePEc Author Service profile, click on "citations" and make appropriate adjustments.:

    as in new window
    1. Ritter, Gunter & Gallegos, MarĂ­a Teresa, 2002. "Bayesian Object Identification: Variants," Journal of Multivariate Analysis, Elsevier, vol. 81(2), pages 301-334, May.
    2. Leiva, Ricardo, 2007. "Linear discrimination with equicorrelated training vectors," Journal of Multivariate Analysis, Elsevier, vol. 98(2), pages 384-409, February.
    Full references (including those not matched with items on IDEAS)

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

    When requesting a correction, please mention this item's handle: RePEc:tsa:wpaper:0053. 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: (Eddie Salinas)

    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.

    This information is provided to you by IDEAS at the Research Division of the Federal Reserve Bank of St. Louis using RePEc data.