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Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs

With the advent of high throughput technology, a huge amount of microRNA information has been added to the growing body of knowledge for non-coding RNAs. Here we present the Dietary MicroRNA Databases (DMD), the first repository for archiving and analyzing the published and novel microRNAs discovere...

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Detalles Bibliográficos
Autores principales: Chiang, Kevin, Shu, Jiang, Zempleni, Janos, Cui, Juan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4451068/
https://www.ncbi.nlm.nih.gov/pubmed/26030752
http://dx.doi.org/10.1371/journal.pone.0128089
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author Chiang, Kevin
Shu, Jiang
Zempleni, Janos
Cui, Juan
author_facet Chiang, Kevin
Shu, Jiang
Zempleni, Janos
Cui, Juan
author_sort Chiang, Kevin
collection PubMed
description With the advent of high throughput technology, a huge amount of microRNA information has been added to the growing body of knowledge for non-coding RNAs. Here we present the Dietary MicroRNA Databases (DMD), the first repository for archiving and analyzing the published and novel microRNAs discovered in dietary resources. Currently there are fifteen types of dietary species, such as apple, grape, cow milk, and cow fat, included in the database originating from 9 plant and 5 animal species. Annotation for each entry, a mature microRNA indexed as DM0000*, covers information of the mature sequences, genome locations, hairpin structures of parental pre-microRNAs, cross-species sequence comparison, disease relevance, and the experimentally validated gene targets. Furthermore, a few functional analyses including target prediction, pathway enrichment and gene network construction have been integrated into the system, which enable users to generate functional insights through viewing the functional pathways and building protein-protein interaction networks associated with each microRNA. Another unique feature of DMD is that it provides a feature generator where a total of 411 descriptive attributes can be calculated for any given microRNAs based on their sequences and structures. DMD would be particularly useful for research groups studying microRNA regulation from a nutrition point of view. The database can be accessed at http://sbbi.unl.edu/dmd/.
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spelling pubmed-44510682015-06-09 Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs Chiang, Kevin Shu, Jiang Zempleni, Janos Cui, Juan PLoS One Research Article With the advent of high throughput technology, a huge amount of microRNA information has been added to the growing body of knowledge for non-coding RNAs. Here we present the Dietary MicroRNA Databases (DMD), the first repository for archiving and analyzing the published and novel microRNAs discovered in dietary resources. Currently there are fifteen types of dietary species, such as apple, grape, cow milk, and cow fat, included in the database originating from 9 plant and 5 animal species. Annotation for each entry, a mature microRNA indexed as DM0000*, covers information of the mature sequences, genome locations, hairpin structures of parental pre-microRNAs, cross-species sequence comparison, disease relevance, and the experimentally validated gene targets. Furthermore, a few functional analyses including target prediction, pathway enrichment and gene network construction have been integrated into the system, which enable users to generate functional insights through viewing the functional pathways and building protein-protein interaction networks associated with each microRNA. Another unique feature of DMD is that it provides a feature generator where a total of 411 descriptive attributes can be calculated for any given microRNAs based on their sequences and structures. DMD would be particularly useful for research groups studying microRNA regulation from a nutrition point of view. The database can be accessed at http://sbbi.unl.edu/dmd/. Public Library of Science 2015-06-01 /pmc/articles/PMC4451068/ /pubmed/26030752 http://dx.doi.org/10.1371/journal.pone.0128089 Text en © 2015 Chiang 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
Chiang, Kevin
Shu, Jiang
Zempleni, Janos
Cui, Juan
Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs
title Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs
title_full Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs
title_fullStr Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs
title_full_unstemmed Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs
title_short Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs
title_sort dietary microrna database (dmd): an archive database and analytic tool for food-borne micrornas
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4451068/
https://www.ncbi.nlm.nih.gov/pubmed/26030752
http://dx.doi.org/10.1371/journal.pone.0128089
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