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    dPORE-miRNA: Polymorphic regulation of microRNA genes

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    Article-PLoS_ONE-dPORE-miRN-2011.pdf
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    Type
    Article
    Authors
    Schmeier, Sebastian cc
    Schaefer, Ulf
    MacPherson, Cameron R.
    Bajic, Vladimir B. cc
    KAUST Department
    Computational Bioscience Research Center (CBRC)
    Bioscience Program
    Applied Mathematics and Computational Science Program
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Date
    2011-02-04
    Permanent link to this record
    http://hdl.handle.net/10754/325287
    
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    Abstract
    Background: MicroRNAs (miRNAs) are short non-coding RNA molecules that act as post-transcriptional regulators and affect the regulation of protein-coding genes. Mostly transcribed by PolII, miRNA genes are regulated at the transcriptional level similarly to protein-coding genes. In this study we focus on human miRNAs. These miRNAs are involved in a variety of pathways and can affect many diseases. Our interest is on possible deregulation of the transcription initiation of the miRNA encoding genes, which is facilitated by variations in the genomic sequence of transcriptional control regions (promoters). Methodology: Our aim is to provide an online resource to facilitate the investigation of the potential effects of single nucleotide polymorphisms (SNPs) on miRNA gene regulation. We analyzed SNPs overlapped with predicted transcription factor binding sites (TFBSs) in promoters of miRNA genes. We also accounted for the creation of novel TFBSs due to polymorphisms not present in the reference genome. The resulting changes in the original TFBSs and potential creation of new TFBSs were incorporated into the Dragon Database of Polymorphic Regulation of miRNA genes (dPORE-miRNA). Conclusions: The dPORE-miRNA database enables researchers to explore potential effects of SNPs on the regulation of miRNAs. dPORE-miRNA can be interrogated with regards to: a/miRNAs (their targets, or involvement in diseases, or biological pathways), b/SNPs, or c/transcription factors. dPORE-miRNA can be accessed at http://cbrc.kaust.edu.sa/dpore and http://apps.sanbi.ac.za/dpore/. Its use is free for academic and non-profit users. © 2011 Schmeier et al.
    Citation
    Schmeier S, Schaefer U, MacPherson CR, Bajic VB (2011) dPORE-miRNA: Polymorphic Regulation of MicroRNA Genes. PLoS ONE 6: e16657. doi:10.1371/journal.pone.0016657.
    Publisher
    Public Library of Science (PLoS)
    Journal
    PLoS ONE
    DOI
    10.1371/journal.pone.0016657
    PubMed ID
    21326606
    PubMed Central ID
    PMC3033892
    ae974a485f413a2113503eed53cd6c53
    10.1371/journal.pone.0016657
    Scopus Count
    Collections
    Articles; Bioscience Program; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

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