APADB: a database for alternative polyadenylation and microRNA regulation events
APADB: a database for alternative polyadenylation and microRNA regulation events
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DOI：
10.1093/database/bau076
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发表时间：
2014-07-22
影响因子：
5.8
通讯作者：
Rotter, Bjoern
中科院分区：
文献类型：
--
作者：
Mueller, Soeren;Rycak, Lukas;Rotter, Bjoern
替代多腺苷酸化 (APA) 是一种广泛的机制，有助于复杂的基因调控动态。大约 50% 的人类蛋白质编码基因含有多个聚腺苷酸化 (PA) 位点；它们的选择性和组合使用产生了 3' 非翻译区 (3'UTR) 长度不同的转录变体。缩短的变异体可以逃避 microRNA (miRNA) 介导的 UTR 调节，尤其是在癌症中，整体 3'UTR 缩短会加速疾病进展、去分化和增殖。在这里，我们介绍 APADB，这是一个通过 3' 末端测序确定的脊椎动物 PA 位点数据库，使用互补 DNA 末端的大量分析。 APADB 为人类、小鼠和鸡基因的编码和非编码转录本提供 (A) PA 位点。对于人类和小鼠，可以使用多种组织类型，包括不同的癌症标本。 APADB 记录预测的 miRNA 结合位点的丢失，并在基因组浏览器中可视化支持每个 PA 位点的下一代测序读数。数据库表可以根据生物体和组织浏览，也可以搜索感兴趣的基因。 APADB 是人类、鸡和小鼠中最大的 APA 数据库。存储的信息为数千个 PA 站点和 APA 事件提供了实验证据。 APADB将3'端测序数据与miRNA结合位点的预测算法相结合，可以进一步改进预测算法。当前数据库缺乏有关 3'UTR 长度的正确信息，尤其是鸡的长度，APADB 提供了必要的信息来弥补这一差距。
Alternative polyadenylation (APA) is a widespread mechanism that contributes to the sophisticated dynamics of gene regulation. Approximately 50% of all protein-coding human genes harbor multiple polyadenylation (PA) sites; their selective and combinatorial use gives rise to transcript variants with differing length of their 3' untranslated region (3'UTR). Shortened variants escape UTR-mediated regulation by microRNAs (miRNAs), especially in cancer, where global 3'UTR shortening accelerates disease progression, dedifferentiation and proliferation. Here we present APADB, a database of vertebrate PA sites determined by 3' end sequencing, using massive analysis of complementary DNA ends. APADB provides (A) PA sites for coding and non-coding transcripts of human, mouse and chicken genes. For human and mouse, several tissue types, including different cancer specimens, are available. APADB records the loss of predicted miRNA binding sites and visualizes next-generation sequencing reads that support each PA site in a genome browser. The database tables can either be browsed according to organism and tissue or alternatively searched for a gene of interest. APADB is the largest database of APA in human, chicken and mouse. The stored information provides experimental evidence for thousands of PA sites and APA events. APADB combines 3' end sequencing data with prediction algorithms of miRNA binding sites, allowing to further improve prediction algorithms. Current databases lack correct information about 3'UTR lengths, especially for chicken, and APADB provides necessary information to close this gap.