dPORE-miRNA: Polymorphic regulation of microRNA genes

Handle URI:
http://hdl.handle.net/10754/325287
Title:
dPORE-miRNA: Polymorphic regulation of microRNA genes
Authors:
Schmeier, Sebastian; Schaefer, Ulf; MacPherson, Cameron R.; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
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.
KAUST Department:
Computational Bioscience Research Center (CBRC)
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
Issue Date:
4-Feb-2011
DOI:
10.1371/journal.pone.0016657
PubMed ID:
21326606
PubMed Central ID:
PMC3033892
Type:
Article
ISSN:
19326203
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorSchmeier, Sebastianen
dc.contributor.authorSchaefer, Ulfen
dc.contributor.authorMacPherson, Cameron R.en
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2014-08-27T09:45:00Z-
dc.date.available2014-08-27T09:45:00Z-
dc.date.issued2011-02-04en
dc.identifier.citationSchmeier 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.en
dc.identifier.issn19326203en
dc.identifier.pmid21326606en
dc.identifier.doi10.1371/journal.pone.0016657en
dc.identifier.urihttp://hdl.handle.net/10754/325287en
dc.description.abstractBackground: 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.en
dc.language.isoenen
dc.publisherPublic Library of Science (PLoS)en
dc.rightsSchmeier et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en
dc.rightsArchived with thanks to PLoS ONEen
dc.subjectmicroRNAen
dc.subjectmicroRNAen
dc.subjectbinding siteen
dc.subjectcomputer interfaceen
dc.subjectcomputer programen
dc.subjectgene controlen
dc.subjectgene sequenceen
dc.subjectgenetic databaseen
dc.subjectpredictionen
dc.subjectpromoter regionen
dc.subjectsingle nucleotide polymorphismen
dc.subjecttranscription initiationen
dc.subjecttranscription regulationen
dc.subjectgene expression regulationen
dc.subjectgenetic databaseen
dc.subjectgenetic polymorphismen
dc.subjectgeneticsen
dc.subjectinformation processingen
dc.subjectmetabolismen
dc.subjectmolecular geneticsen
dc.subjectnucleotide sequenceen
dc.subjectphysiologyen
dc.subjectraten
dc.subjectBase Sequenceen
dc.subjectData Collectionen
dc.subjectDatabases, Geneticen
dc.subjectGene Expression Regulationen
dc.subjectMicroRNAsen
dc.subjectMolecular Sequence Dataen
dc.subjectPolymorphism, Geneticen
dc.subjectPolymorphism, Single Nucleotideen
dc.subjectPromoter Regions, Geneticen
dc.subjectRatsen
dc.subjectSoftwareen
dc.subjectUser-Computer Interfaceen
dc.titledPORE-miRNA: Polymorphic regulation of microRNA genesen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC3033892en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionUnidad Académica de Sistemas Arrecifales (Puerto Morelos), Instituto de Ciencias Del Mar y Limnología, Universidad Nacional Autõnoma de México, Puerto Morelos, QR 77580, Mexicoen
dc.contributor.institutionSchool of Natural Sciences, University of California Merced, 5200 North Lake Road, Merced, CA 95343, United Statesen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorSchmeier, Sebastianen
kaust.authorMacPherson, Cameron R.en
kaust.authorBajic, Vladimir B.en
kaust.authorSchaefer, Ulfen

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