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

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Abstract

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.

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Most cited references 18

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

Eric Huntzinger, Elisa Izaurralde (2011)

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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miRBase: microRNA sequences, targets and gene nomenclature

Sam Griffiths-Jones, Russell J. Grocock, Stijn van Dongen … (2005)

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

Ioannis S Vlachos, Maria D. Paraskevopoulou, Dimitra Karagkouni … (2014)

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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Journal

Journal ID (iso-abbrev): BMC Bioinformatics

Title: BMC bioinformatics

Publisher: Springer Science and Business Media LLC

ISSN (Electronic): 1471-2105

ISSN (Print): 1471-2105

Publication date (Electronic): Dec 31 2018

Volume: 19

Issue: Suppl 19

Affiliations

[1 ] Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.

[2 ] School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095 Adelaide, Australia.

[3 ] School of Engineering, Dali University, Dali, 671003, China.

[4 ] Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, United States.

[5 ] National Engineering Research Center of Communications and Networking, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.

[6 ] School of Computer and Information, Hefei University of Technology, Hefei, 230009, China.

[7 ] School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095 Adelaide, Australia. Thuc.Le@unisa.edu.au.

[8 ] Centre for Cancer Biology, University of South Australia, SA, 5000 Adelaide, Australia. Thuc.Le@unisa.edu.au.

Article

Publisher Item ID: 10.1186/s12859-018-2531-5

DOI: 10.1186/s12859-018-2531-5

PMC ID: 6311916

PubMed ID: 30598108

SO-VID: bc3e77d2-fe25-4fb3-afbe-976ad54de1e2

History

Keywords: Annotation,Bioinformatics,miRBase repository,miRNA,miRNA family,miRNA information retrieval

Data availability:

Keywords: Annotation, Bioinformatics, miRBase repository, miRNA, miRNA family, miRNA information retrieval

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

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Most cited references 18

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

miRBase: microRNA sequences, targets and gene nomenclature

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

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