miRBase: microRNA gene nomenclature sequences and targets

miRBase：microRNA 基因命名序列和靶标

• 批准号: BB/G022623/1
• 负责人: Sam Griffiths-Jones
• 金额: $ 60.37万
• 依托单位: University of Manchester
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2009
• 资助国家: 英国
• 起止时间: 2009 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FG022623%2F1
• 关键词: miRBase; microRNA; gene; nomenclature; sequences

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.

microRNA是微小的RNA分子，由microRNA基因表达，调节动物基因组中三分之一到一半基因的表达。在动物和植物基因组中广泛存在的microRNA直到2001年才被发现。miRBase数据库随后建立，为microRNA社区提供一系列服务。特别是，miRBase在科学文献中发表之前会秘密地为新发现的microRNA命名。这确保了相同的microRNA在描述它的每篇论文中获得相同的名称，更重要的是，不同的microRNA永远不会被称为相同的名称。独立管理的协调命名方案使该领域的巨大增长。miRBase还存储和分发所有已发表的microRNA序列，以及描述它们的参考文献，它们在基因组中的位置，关于它们功能的信息以及其他相关序列。这些服务很快就成为microRNA社区的必需品。新的microRNA序列的发现一直在继续，最近几个月随着新测序技术的使用而显着增加。该数据库目前包含8500多个条目，过去2年增加了4000多个。该提案为管理和推动microRNA生物学发现的下一阶段提供了资源。特别是，我们将开发新的界面，允许microRNA生物学家向数据库提供有关任何microRNA的信息。我们将扩大数据库中的microRNA序列集，以包括目前不符合严格纳入标准的候选人和预测，并提供有关其可靠性的具体信息。我们将开发一个系统，半自动地为新的microRNA命名。除了发现所有基因组中的所有microRNA外，该社区还专注于建立每个microRNA的目标。相对较少的microRNA具有实验验证的靶点，但有几个小组通过网络提供了预测的靶点。我们将开发一种服务，将这些预测与已知的靶基因聚合在一起。我们还将制作一个界面，允许研究人员将实验确定的靶基因提交到数据库。miRBase中的所有数据都可以在网上找到，也可以通过FTP下载。该网站每周收到10万到30万的页面访问量，描述miRBase的论文已被650多份科学出版物引用。

项目成果

miRBase: annotating high confidence microRNAs using deep sequencing data.

• DOI: 10.1093/nar/gkt1181
• 发表时间: 2014-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Kozomara A;Griffiths-Jones S
• 通讯作者: Griffiths-Jones S

Reducing ligation bias of small RNAs in libraries for next generation sequencing.

• DOI: 10.1186/1758-907x-3-4
• 发表时间: 2012-05-30
• 期刊: Silence
• 作者: Sorefan K;Pais H;Hall AE;Kozomara A;Griffiths-Jones S;Moulton V;Dalmay T
• 通讯作者: Dalmay T

miRBase: integrating microRNA annotation and deep-sequencing data.

• DOI: 10.1093/nar/gkq1027
• 发表时间: 2011-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Kozomara A;Griffiths-Jones S
• 通讯作者: Griffiths-Jones S

Sex-biased expression of microRNAs in Schistosoma mansoni.

• DOI: 10.1371/journal.pntd.0002402
• 发表时间: 2013
• 期刊: PLoS neglected tropical diseases
• 影响因子: 3.8
• 作者: Marco A;Kozomara A;Hui JH;Emery AM;Rollinson D;Griffiths-Jones S;Ronshaugen M
• 通讯作者: Ronshaugen M

Target repression induced by endogenous microRNAs: large differences, small effects.

• DOI: 10.1371/journal.pone.0104286
• 发表时间: 2014
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Kozomara A;Hunt S;Ninova M;Griffiths-Jones S;Ronshaugen M
• 通讯作者: Ronshaugen M