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microPIR: An Integrated Database of MicroRNA Target Sites within Human Promoter Sequences
BACKGROUND: microRNAs are generally understood to regulate gene expression through binding to target sequences within 3′-UTRs of mRNAs. Therefore, computational prediction of target sites is usually restricted to these gene regions. Recent experimental studies though have suggested that microRNAs ma...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306312/ https://www.ncbi.nlm.nih.gov/pubmed/22439011 http://dx.doi.org/10.1371/journal.pone.0033888 |
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author | Piriyapongsa, Jittima Bootchai, Chaiwat Ngamphiw, Chumpol Tongsima, Sissades |
author_facet | Piriyapongsa, Jittima Bootchai, Chaiwat Ngamphiw, Chumpol Tongsima, Sissades |
author_sort | Piriyapongsa, Jittima |
collection | PubMed |
description | BACKGROUND: microRNAs are generally understood to regulate gene expression through binding to target sequences within 3′-UTRs of mRNAs. Therefore, computational prediction of target sites is usually restricted to these gene regions. Recent experimental studies though have suggested that microRNAs may alternatively modulate gene expression by interacting with promoters. A database of potential microRNA target sites in promoters would stimulate research in this field leading to more understanding of complex microRNA regulatory mechanism. METHODOLOGY: We developed a database hosting predicted microRNA target sites located within human promoter sequences and their associated genomic features, called microPIR (microRNA-Promoter Interaction Resource). microRNA seed sequences were used to identify perfect complementary matching sequences in the human promoters and the potential target sites were predicted using the RNAhybrid program. >15 million target sites were identified which are located within 5000 bp upstream of all human genes, on both sense and antisense strands. The experimentally confirmed argonaute (AGO) binding sites and EST expression data including the sequence conservation across vertebrate species of each predicted target are presented for researchers to appraise the quality of predicted target sites. The microPIR database integrates various annotated genomic sequence databases, e.g. repetitive elements, transcription factor binding sites, CpG islands, and SNPs, offering users the facility to extensively explore relationships among target sites and other genomic features. Furthermore, functional information of target genes including gene ontologies, KEGG pathways, and OMIM associations are provided. The built-in genome browser of microPIR provides a comprehensive view of multidimensional genomic data. Finally, microPIR incorporates a PCR primer design module to facilitate experimental validation. CONCLUSIONS: The proposed microPIR database is a useful integrated resource of microRNA-promoter target interactions for experimental microRNA researchers and computational biologists to study the microRNA regulation through gene promoter. The database can be freely accessed from: http://www4a.biotec.or.th/micropir. |
format | Online Article Text |
id | pubmed-3306312 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-33063122012-03-21 microPIR: An Integrated Database of MicroRNA Target Sites within Human Promoter Sequences Piriyapongsa, Jittima Bootchai, Chaiwat Ngamphiw, Chumpol Tongsima, Sissades PLoS One Research Article BACKGROUND: microRNAs are generally understood to regulate gene expression through binding to target sequences within 3′-UTRs of mRNAs. Therefore, computational prediction of target sites is usually restricted to these gene regions. Recent experimental studies though have suggested that microRNAs may alternatively modulate gene expression by interacting with promoters. A database of potential microRNA target sites in promoters would stimulate research in this field leading to more understanding of complex microRNA regulatory mechanism. METHODOLOGY: We developed a database hosting predicted microRNA target sites located within human promoter sequences and their associated genomic features, called microPIR (microRNA-Promoter Interaction Resource). microRNA seed sequences were used to identify perfect complementary matching sequences in the human promoters and the potential target sites were predicted using the RNAhybrid program. >15 million target sites were identified which are located within 5000 bp upstream of all human genes, on both sense and antisense strands. The experimentally confirmed argonaute (AGO) binding sites and EST expression data including the sequence conservation across vertebrate species of each predicted target are presented for researchers to appraise the quality of predicted target sites. The microPIR database integrates various annotated genomic sequence databases, e.g. repetitive elements, transcription factor binding sites, CpG islands, and SNPs, offering users the facility to extensively explore relationships among target sites and other genomic features. Furthermore, functional information of target genes including gene ontologies, KEGG pathways, and OMIM associations are provided. The built-in genome browser of microPIR provides a comprehensive view of multidimensional genomic data. Finally, microPIR incorporates a PCR primer design module to facilitate experimental validation. CONCLUSIONS: The proposed microPIR database is a useful integrated resource of microRNA-promoter target interactions for experimental microRNA researchers and computational biologists to study the microRNA regulation through gene promoter. The database can be freely accessed from: http://www4a.biotec.or.th/micropir. Public Library of Science 2012-03-16 /pmc/articles/PMC3306312/ /pubmed/22439011 http://dx.doi.org/10.1371/journal.pone.0033888 Text en Piriyapongsa et al. http://creativecommons.org/licenses/by/4.0/ 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 properly credited. |
spellingShingle | Research Article Piriyapongsa, Jittima Bootchai, Chaiwat Ngamphiw, Chumpol Tongsima, Sissades microPIR: An Integrated Database of MicroRNA Target Sites within Human Promoter Sequences |
title | microPIR: An Integrated Database of MicroRNA Target Sites within Human Promoter Sequences |
title_full | microPIR: An Integrated Database of MicroRNA Target Sites within Human Promoter Sequences |
title_fullStr | microPIR: An Integrated Database of MicroRNA Target Sites within Human Promoter Sequences |
title_full_unstemmed | microPIR: An Integrated Database of MicroRNA Target Sites within Human Promoter Sequences |
title_short | microPIR: An Integrated Database of MicroRNA Target Sites within Human Promoter Sequences |
title_sort | micropir: an integrated database of microrna target sites within human promoter sequences |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306312/ https://www.ncbi.nlm.nih.gov/pubmed/22439011 http://dx.doi.org/10.1371/journal.pone.0033888 |
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