miRBase: microRNA gene nomenclature sequences and targets

Lead Research Organisation: University of Manchester
Department Name: Life Sciences


MicroRNAs are tiny RNA molecules, expressed from microRNA genes, that regulate the expression of a third to a half of all genes in an animal's genome. The widespread occurrence of microRNAs in animal and plant genomes was only discovered in 2001. The miRBase database was established soon afterwards to provide a range of services to the microRNA community. In particular, miRBase confidentially assigns names to novel microRNA discoveries before they are published in the scientific literature. This assures that the same microRNA receives the same name in each paper that describes it, and more importantly, that different microRNAs are never referred to by the same name. The independent management of a coordinated naming scheme has allowed the enormous growth of the field. miRBase also stores and distributes all published microRNA sequences, together with the references that describe them, their locations in the genome, information about their function, and other related sequences. These services have quickly become entirely essential to the microRNA community. The discovery of novel microRNA sequences has continued at pace, increasing significantly in recent months with the use of new sequencing technologies. The database currently contains over 8500 entries, an increase of over 4000 in the past 2 years. This proposal provides the resources to manage and drive the next phase of microRNA biological discovery. In particular, we will develop new interfaces that allow the microRNA biologist to contribute information about any microRNA to the database. We will expand the set of microRNA sequences in the database to include candidates and predictions that currently do not meet the strict criteria for inclusion, and provide specific information about their reliability. We will develop a system that assigns names to new microRNAs semi-automatically. Alongside the drive to discover all microRNAs in all genomes, the community is focused on establishing the targets of every microRNA. Relatively few microRNAs have experimentally validated targets, but several groups provide predicted targets via the web. We will develop a service that aggregates these predictions, together with the known target genes. We will also produce an interface that allows researchers to submit experimentally determined target genes to the database. All data in miRBase are available on the web, and for download by FTP. The website receives between 100000 and 300000 page views each week, and the papers that describe miRBase have been cited in over 650 scientific publications.

Technical Summary

miRBase is an online database that provides a range of services and resources to the rapidly-growing microRNA community. miRBase (previously called the microRNA Registry) was established in 2002 with the primary aim to independently assign gene names to novel microRNAs prior to their publication. miRBase is also the central repository of all published microRNA sequences, their associated literature references, genomic coordinates, and functional annotation. The establishment of a sensible curated nomenclature scheme and provision of a focused data resource, with the support of the microRNA community, have been critical factors in the explosive growth of the microRNA field. Many derived databases and resources exist, including for downstream analysis and commercially produced arrays and detection kits; all depend on the miRBase database. This proposal provides for the continued development of miRBase, to take account of increased rates of microRNA gene discovery from new technologies (such as high-throughput sequencing) and to position the database as a long-term and stable community resource. Developments proposed here include interfaces for community annotation of microRNA sequences and function, expansion to include microRNA candidates and predictions, and interfaces to aggregate microRNA target predictions from all available external sources. miRBase continues to drive the possibilities for microRNA genomics and sequence analysis.


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Description We have developed a public database (miRBase) for a class of genes called microRNAs. This database is the central repository for all new microRNA sequences and we are responsible for naming all microRNA genes as they are discovered. The work funded on this grant enabled a number of improvements to be made to the database and the website through which it is accessed. In particular, we incorporated novel data types, primarily deep sequencing data, to allow the user to query expression of microRNAs in different tissues, and to the judge the validity of previous microRNA annotations.
Exploitation Route The miRBase database is used by >20000 researchers, in both academia and industry, every month. The uses are varied, including the commercial development of kits and tools for microRNA research, and testing of microRNAs for clinical applications. All such work world-wide starts from sequences available in the miRBase database.
Sectors Agriculture, Food and Drink,Education,Pharmaceuticals and Medical Biotechnology

URL http://www.mirbase.org/
Description The miRBase database is used by >20000 researchers each month, from both academia and commercial sectors. The papers describing miRBase have been cited >15000 times. The uses are wide-ranging, but include commercial development of kits and tools for microRNA research, and investigation of clinical applications of microRNA work. All microRNA studies start from miRBase sequence data.
First Year Of Impact 2003
Sector Agriculture, Food and Drink,Education,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

Description Bioinformatics and Biological Resources Fund
Amount £580,038 (GBP)
Funding ID BB/M011275/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2015 
End 02/2020
Title miRBase 
Description miRBase is the primary database of microRNA sequences and annotation. http://mirbase.org/ 
Type Of Material Database/Collection of data 
Provided To Others? Yes  
Impact miRBase is used by microRNA researchers worldwide. The website has more than 20000 unique users per month, and the papers describing miRBase have been cited more than 15000 times. 
URL http://mirbase.org/