• Login
    View Item 
    •   Home
    • Research
    • Articles
    • View Item
    •   Home
    • Research
    • Articles
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of KAUSTCommunitiesIssue DateSubmit DateThis CollectionIssue DateSubmit Date

    My Account

    Login

    Quick Links

    Open Access PolicyORCID LibguidePlumX LibguideSubmit an Item

    Statistics

    Display statistics

    A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites

    • CSV
    • RefMan
    • EndNote
    • BibTex
    • RefWorks
    Type
    Article
    Authors
    Kulakovskiy, Ivan V.
    Belostotsky, A. A.
    Kasianov, Artem S.
    Esipova, Natalia G.
    Medvedeva, Yulia
    Eliseeva, Irina A.
    Makeev, Vsevolod J.
    KAUST Department
    Computational Bioscience Research Center (CBRC)
    Date
    2011-08-18
    Online Publication Date
    2011-08-18
    Print Publication Date
    2011-10-01
    Permanent link to this record
    http://hdl.handle.net/10754/561843
    
    Metadata
    Show full item record
    Abstract
    Motivation: Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding of the transcription regulatory code. Results: We constructed binding motifs for TFs forming a complex with HIF-1α at the erythropoietin 3'-enhancer. Corresponding TFBSs were predicted in the segments around transcription start sites (TSSs) of all human genes. Using the genome-wide set of regulatory regions, we observed several strongly preferred distances between hypoxia-responsive element (HRE) and binding sites of a particular cofactor protein. The set of preferred distances was called as a preferred pair distance template (PPDT). PPDT dramatically depended on the TF and orientation of its binding sites relative to HRE. PPDT evaluated from the genome-wide set of regulatory sequences was used to detect significant PPDT-consistent binding site pairs in regulatory regions of hypoxia-responsive genes. We believe PPDT can help to reveal the layout of eukaryotic regulatory segments. © The Author 2011. Published by Oxford University Press. All rights reserved.
    Publisher
    Oxford University Press (OUP)
    Journal
    Bioinformatics
    DOI
    10.1093/bioinformatics/btr453
    PubMed ID
    21852305
    ae974a485f413a2113503eed53cd6c53
    10.1093/bioinformatics/btr453
    Scopus Count
    Collections
    Articles; Computational Bioscience Research Center (CBRC)

    entitlement

    Related articles

    • Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules.
    • Authors: Acevedo-Luna N, Mariño-Ramírez L, Halbert A, Hansen U, Landsman D, Spouge JL
    • Issue date: 2016 Nov 21
    • Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model.
    • Authors: Oliver P, Peralta-Gil M, Tabche ML, Merino E
    • Issue date: 2016 Aug 27
    • Transcription factor-DNA binding: beyond binding site motifs.
    • Authors: Inukai S, Kock KH, Bulyk ML
    • Issue date: 2017 Apr
    • Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.
    • Authors: Makeev VJ, Lifanov AP, Nazina AG, Papatsenko DA
    • Issue date: 2003 Oct 15
    • The GCN4 bZIP can bind to noncognate gene regulatory sequences.
    • Authors: Fedorova AV, Chan IS, Shin JA
    • Issue date: 2006 Jul
    DSpace software copyright © 2002-2021  DuraSpace
    Quick Guide | Contact Us | Send Feedback
    Open Repository is a service hosted by 
    Atmire NV
     

    Export search results

    The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format.

    By default, clicking on the export buttons will result in a download of the allowed maximum amount of items. For anonymous users the allowed maximum amount is 50 search results.

    To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export.

    After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.