Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

miRBase (microRNA dababase)

General information

Description: miRBase is the central repository for microRNA (miRNA) sequence information. miRBase has a role in defining the nomenclature for miRNA genes and assigning names to novel miRNAs for publication in peer-reviewed journals. The online miRBase database is a resource containing all published miRNA sequences, together with textual annotation and links to the primary literature and to other secondary databases. The database provides a variety of methods to query the data, by specific searches of sequences and associated text and literature.
Year founded: 2004
Last update: 2018-03
Version: v22.0
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United Kingdom
Data type:
RNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: The University of Manchester
Address: Manchester, M13 9PT, UK
City: Manchester
Province/State:
Country/Region: United Kingdom
Contact name (PI/Team): Sam Griffiths-Jones
Contact email (PI/Helpdesk): sam.griffiths-jones@manchester.ac.uk

Record metadata

Created on: 2015-06-20
Curated by:
Dong Zou [2019-01-12]
Nashaiman Pervaiz [2018-12-28]
Lina Ma [2018-06-07]
Lin Liu [2016-03-30]
Lin Liu [2016-03-29]
Zhang Zhang [2016-01-18]
Zhang Zhang [2015-12-18]
Li Yang [2015-06-26]

Ranking

All databases:
11/4548 (99.78%)
Standard ontology and nomenclature:
2/182 (99.451%)
Gene genome and annotation:
7/1211 (99.505%)
11
Total Rank
10,101
Citations
631.312
z-index

Community reviews

Not Rated
Data quality & quantity:
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System accessibility & reliability:

Word cloud

Publications

30423142
miRBase: from microRNA sequences to function. [PMID: 30423142]
Kozomara A, Birgaoanu M, Griffiths-Jones S.

miRBase catalogs, names and distributes microRNA gene sequences. The latest release of miRBase (v22) contains microRNA sequences from 271 organisms: 38 589 hairpin precursors and 48 860 mature microRNAs. We describe improvements to the database and website to provide more information about the quality of microRNA gene annotations, and the cellular functions of their products. We have collected 1493 small RNA deep sequencing datasets and mapped a total of 5.5 billion reads to microRNA sequences. The read mapping patterns provide strong support for the validity of between 20% and 65% of microRNA annotations in different well-studied animal genomes, and evidence for the removal of >200 sequences from the database. To improve the availability of microRNA functional information, we are disseminating Gene Ontology terms annotated against miRBase sequences. We have also used a text-mining approach to search for microRNA gene names in the full-text of open access articles. Over 500 000 sentences from 18 542 papers contain microRNA names. We score these sentences for functional information and link them with 12 519 microRNA entries. The sentences themselves, and word clouds built from them, provide effective summaries of the functional information about specific microRNAs. miRBase is publicly and freely available at http://mirbase.org/.

Nucleic Acids Res. 2019:47(D1) | 67 Citations (from Europe PMC, 2020-05-30)
24275495
miRBase: annotating high confidence microRNAs using deep sequencing data. [PMID: 24275495]
Kozomara A, Griffiths-Jones S.

We describe an update of the miRBase database (http://www.mirbase.org/), the primary microRNA sequence repository. The latest miRBase release (v20, June 2013) contains 24 521 microRNA loci from 206 species, processed to produce 30 424 mature microRNA products. The rate of deposition of novel microRNAs and the number of researchers involved in their discovery continue to increase, driven largely by small RNA deep sequencing experiments. In the face of these increases, and a range of microRNA annotation methods and criteria, maintaining the quality of the microRNA sequence data set is a significant challenge. Here, we describe recent developments of the miRBase database to address this issue. In particular, we describe the collation and use of deep sequencing data sets to assign levels of confidence to miRBase entries. We now provide a high confidence subset of miRBase entries, based on the pattern of mapped reads. The high confidence microRNA data set is available alongside the complete microRNA collection at http://www.mirbase.org/. We also describe embedding microRNA-specific Wikipedia pages on the miRBase website to encourage the microRNA community to contribute and share textual and functional information.

Nucleic Acids Res. 2014:42(Database issue) | 2095 Citations (from Europe PMC, 2020-05-30)
21037258
miRBase: integrating microRNA annotation and deep-sequencing data. [PMID: 21037258]
Kozomara A, Griffiths-Jones S.

miRBase is the primary online repository for all microRNA sequences and annotation. The current release (miRBase 16) contains over 15,000 microRNA gene loci in over 140 species, and over 17,000 distinct mature microRNA sequences. Deep-sequencing technologies have delivered a sharp rise in the rate of novel microRNA discovery. We have mapped reads from short RNA deep-sequencing experiments to microRNAs in miRBase and developed web interfaces to view these mappings. The user can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression. These data can be used as a proxy for relative expression levels of microRNA sequences, provide detailed evidence for microRNA annotations and alternative isoforms of mature microRNAs, and allow us to revisit previous annotations. miRBase is available online at: http://www.mirbase.org/.

Nucleic Acids Res. 2011:39(Database issue) | 1937 Citations (from Europe PMC, 2020-05-30)
20205188
miRBase: microRNA sequences and annotation. [PMID: 20205188]
Griffiths-Jones S.

miRBase is the central repository for microRNA (miRNA) sequence information. miRBase has a role in defining the nomenclature for miRNA genes and assigning names to novel miRNAs for publication in peer-reviewed journals. The online miRBase database is a resource containing all published miRNA sequences, together with textual annotation and links to the primary literature and to other secondary databases. The database provides a variety of methods to query the data, by specific searches of sequences and associated text and literature. All miRBase data are also available for download from the miRBase FTP site. (c) 2010 by John Wiley & Sons, Inc.

Curr Protoc Bioinformatics. 2010:Chapter 12() | 33 Citations (from Europe PMC, 2020-05-30)
17991681
miRBase: tools for microRNA genomics. [PMID: 17991681]
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ.

miRBase is the central online repository for microRNA (miRNA) nomenclature, sequence data, annotation and target prediction. The current release (10.0) contains 5071 miRNA loci from 58 species, expressing 5922 distinct mature miRNA sequences: a growth of over 2000 sequences in the past 2 years. miRBase provides a range of data to facilitate studies of miRNA genomics: all miRNAs are mapped to their genomic coordinates. Clusters of miRNA sequences in the genome are highlighted, and can be defined and retrieved with any inter-miRNA distance. The overlap of miRNA sequences with annotated transcripts, both protein- and non-coding, are described. Finally, graphical views of the locations of a wide range of genomic features in model organisms allow for the first time the prediction of the likely boundaries of many miRNA primary transcripts. miRBase is available at http://microrna.sanger.ac.uk/.

Nucleic Acids Res. 2008:36(Database issue) | 2261 Citations (from Europe PMC, 2020-05-30)
16381832
miRBase: microRNA sequences, targets and gene nomenclature. [PMID: 16381832]
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ.

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 http://microrna.sanger.ac.uk/.

Nucleic Acids Res. 2006:34(Database issue) | 2275 Citations (from Europe PMC, 2020-05-30)
16957372
miRBase: the microRNA sequence database. [PMID: 16957372]
Griffiths-Jones S.

The miRBase Sequence database is the primary repository for published microRNA (miRNA) sequence and annotation data. miRBase provides a user-friendly web interface for miRNA data, allowing the user to search using key words or sequences, trace links to the primary literature referencing the miRNA discoveries, analyze genomic coordinates and context, and mine relationships between miRNA sequences. miRBase also provides a confidential gene-naming service, assigning official miRNA names to novel genes before their publication. The methods outlined in this chapter describe these functions. miRBase is freely available to all at http://microrna.sanger.ac.uk/.

Methods Mol Biol. 2006:342() | 310 Citations (from Europe PMC, 2020-05-30)
14681370
The microRNA Registry. [PMID: 14681370]
Griffiths-Jones S.

The miRNA Registry provides a service for the assignment of miRNA gene names prior to publication. A comprehensive and searchable database of published miRNA sequences is accessible via a web interface (http://www.sanger.ac.uk/Software/Rfam/mirna/), and all sequence and annotation data are freely available for download. Release 2.0 of the database contains 506 miRNA entries from six organisms.

Nucleic Acids Res. 2004:32(Database issue) | 1123 Citations (from Europe PMC, 2020-05-30)