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      Is Open Access

      miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase

      research-article
      1 , 1 , 2 , 3 , 1 , 2 , 4 , 5 , 6 , 2 , 2 , 7 ,
      BMC Bioinformatics
      BioMed Central
      29th International Conference on Genome Informatics
      3-5 December 2018
      miRNA, miRBase repository, Annotation, miRNA information retrieval, miRNA family, Bioinformatics

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          Abstract

          Background

          miRBase is the primary repository for published miRNA sequence and annotation data, and serves as the “go-to” place for miRNA research. However, the definition and annotation of miRNAs have been changed significantly across different versions of miRBase. The changes cause inconsistency in miRNA related data between different databases and articles published at different times. Several tools have been developed for different purposes of querying and converting the information of miRNAs between different miRBase versions, but none of them individually can provide the comprehensive information about miRNAs in miRBase and users will need to use a number of different tools in their analyses.

          Results

          We introduce miRBaseConverter, an R package integrating the latest miRBase version 22 available in Bioconductor to provide a suite of functions for converting and retrieving miRNA name (ID), accession, sequence, species, version and family information in different versions of miRBase. The package is implemented in R and available under the GPL-2 license from the Bioconductor website ( http://bioconductor.org/packages/miRBaseConverter/). A Shiny-based GUI suitable for non-R users is also available as a standalone application from the package and also as a web application at http://nugget.unisa.edu.au:3838/miRBaseConverter. miRBaseConverter has a built-in database for querying miRNA information in all species and for both pre-mature and mature miRNAs defined by miRBase. In addition, it is the first tool for batch querying the miRNA family information. The package aims to provide a comprehensive and easy-to-use tool for miRNA research community where researchers often utilize published miRNA data from different sources.

          Conclusions

          The Bioconductor package miRBaseConverter and the Shiny-based web application are presented to provide a suite of functions for converting and retrieving miRNA name, accession, sequence, species, version and family information in different versions of miRBase. The package will serve a wide range of applications in miRNA research and could provide a full view of the miRNAs of interest.

          Electronic supplementary material

          The online version of this article (10.1186/s12859-018-2531-5) contains supplementary material, which is available to authorized users.

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          Most cited references18

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          Gene silencing by microRNAs: contributions of translational repression and mRNA decay.

          Despite their widespread roles as regulators of gene expression, important questions remain about target regulation by microRNAs. Animal microRNAs were originally thought to repress target translation, with little or no influence on mRNA abundance, whereas the reverse was thought to be true in plants. Now, however, it is clear that microRNAs can induce mRNA degradation in animals and, conversely, translational repression in plants. Recent studies have made important advances in elucidating the relative contributions of these two different modes of target regulation by microRNAs. They have also shed light on the specific mechanisms of target silencing, which, although it differs fundamentally between plants and animals, shares some common features between the two kingdoms.
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            • Record: found
            • Abstract: found
            • Article: not found

            miRBase: microRNA sequences, targets and gene nomenclature

            The miRBase database aims to provide integrated interfaces to comprehensive microRNA sequence data, annotation and predicted gene targets. miRBase takes over functionality from the microRNA Registry and fulfils three main roles: the miRBase Registry acts as an independent arbiter of microRNA gene nomenclature, assigning names prior to publication of novel miRNA sequences. miRBase Sequences is the primary online repository for miRNA sequence data and annotation. miRBase Targets is a comprehensive new database of predicted miRNA target genes. miRBase is available at .
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              • Record: found
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              Is Open Access

              DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions

              microRNAs (miRNAs) are short non-coding RNA species, which act as potent gene expression regulators. Accurate identification of miRNA targets is crucial to understanding their function. Currently, hundreds of thousands of miRNA:gene interactions have been experimentally identified. However, this wealth of information is fragmented and hidden in thousands of manuscripts and raw next-generation sequencing data sets. DIANA-TarBase was initially released in 2006 and it was the first database aiming to catalog published experimentally validated miRNA:gene interactions. DIANA-TarBase v7.0 (http://www.microrna.gr/tarbase) aims to provide for the first time hundreds of thousands of high-quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data. DIANA-TarBase v7.0 enables users to easily identify positive or negative experimental results, the utilized experimental methodology, experimental conditions including cell/tissue type and treatment. The new interface provides also advanced information ranging from the binding site location, as identified experimentally as well as in silico, to the primer sequences used for cloning experiments. More than half a million miRNA:gene interactions have been curated from published experiments on 356 different cell types from 24 species, corresponding to 9- to 250-fold more entries than any other relevant database. DIANA-TarBase v7.0 is freely available.
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                Author and article information

                Contributors
                taosheng.x@gmail.com
                oksuning@mail.ustc.edu.cn
                Lin.Liu@unisa.edu.au
                weijia.zhang@unisa.edu.au
                Jiuyong.Li@unisa.edu.au
                Thuc.Le@unisa.edu.au
                Conference
                BMC Bioinformatics
                BMC Bioinformatics
                BMC Bioinformatics
                BioMed Central (London )
                1471-2105
                31 December 2018
                31 December 2018
                2018
                : 19
                Issue : Suppl 19 Issue sponsor : Publication of this supplement has not been supported by sponsorship. Information about the source of funding for publication charges can be found in the individual articles. The articles have undergone the journal's standard peer review process for supplements. JZ was not involved in the review decision of their paper. No other competing interests were declared.
                : 514
                Affiliations
                [1 ]ISNI 0000 0004 1806 6366, GRID grid.467850.8, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, ; Hefei, 230031 China
                [2 ]ISNI 0000 0000 8994 5086, GRID grid.1026.5, School of Information Technology and Mathematical Sciences, University of South Australia, ; Mawson Lakes, SA, 5095 Adelaide Australia
                [3 ]GRID grid.440682.c, School of Engineering, Dali University, ; Dali, 671003 China
                [4 ]ISNI 0000000086837370, GRID grid.214458.e, Department of Computational Medicine and Bioinformatics, University of Michigan, ; Ann Arbor, 48109 United States
                [5 ]ISNI 0000 0004 0369 3615, GRID grid.453246.2, National Engineering Research Center of Communications and Networking, Nanjing University of Posts and Telecommunications, ; Nanjing, 210023 China
                [6 ]GRID grid.256896.6, School of Computer and Information, Hefei University of Technology, ; Hefei, 230009 China
                [7 ]ISNI 0000 0004 0450 082X, GRID grid.470344.0, Centre for Cancer Biology, University of South Australia, ; SA, 5000 Adelaide Australia
                Article
                2531
                10.1186/s12859-018-2531-5
                6311916
                30598108
                bc3e77d2-fe25-4fb3-afbe-976ad54de1e2
                © The Author(s) 2018

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                29th International Conference on Genome Informatics
                Yunnan, China
                3-5 December 2018
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                © The Author(s) 2018

                Bioinformatics & Computational biology
                mirna,mirbase repository,annotation,mirna information retrieval,mirna family,bioinformatics

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