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. 2015 Jun 1;10(6):e0128089.
doi: 10.1371/journal.pone.0128089. eCollection 2015.

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

Kevin Chiang  1 , Jiang Shu  1 , Janos Zempleni  2 , Juan Cui  1
Affiliations

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

Kevin Chiang et al. PLoS One. .

Abstract

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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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. DMD construction workflow and the outline of data content.
Fig 2
Fig 2. Illustration of searching "bta-mir-29b" and the search results.
Fig 3
Fig 3. The DMD entry for 'bta-mir-29b,' which contains sequence information, precursor annotation, and homologous sequences and their associated targets and diseases.
Fig 4
Fig 4. Clockwise from top: "bta-mir-29b” shows 645 targets; the protein-protein network visualization; and the gene enrichment analysis and pathway information.
Fig 5
Fig 5. The feature generation page showing the entry of “bta-mir-29b” in fasta format and its output in a tab separated values format.
See this image and copyright information in PMC

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