ARED-Plus: an updated and expanded database of AU-rich element-containing mRNAs and pre-mRNAs
ARED-Plus: an updated and expanded database of AU-rich element-containing mRNAs and pre-mRNAs
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DOI：
10.1093/nar/gkx975
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Khabar, Khalid S. A.
中科院分区：
文献类型：
--
作者：
Bakheet, Tala;Hitti, Edward;Khabar, Khalid S. A.
在这里，我们提出了一个更新版本的AU丰富的元素数据库（ARED-Plus），可在http://brp.kfshrc.edu.sa/ared免费获得。战神是保守序列元件，首次在哺乳动物转录本的3 'UTR中发现。在过去的几年里，我们编制了一系列ARE数据库，揭示了ARE基因的范围和广泛分布。对于此次更新，我们采用了优化的搜索算法，在ARE选择中提高了特异性和灵敏度。通过将ARE簇的数目与重叠的AUUUA五聚体的数目直接相关来简化不同ARE簇的指定。此外，新的数据库被扩展到包括具有内含子战神（前mRNA）的基因及其特征，因为最近的观察报告了它们的丰度和生物学意义。加入了一些增强功能，如自定义列视图，额外的搜索选项和实时搜索功能。新版本包括AREsite和AREScore的链接，这是两个相关的ARE评估算法，用于进一步评估ARE特征。ARED-Plus现在包含了人类转录组中更新的战神库，可能在几个研究领域有用。
Here we present an updated version of the AU-Rich Element Database (ARED-Plus) that is freely available at http://brp.kfshrc.edu.sa/ared. AREs are conserved sequence elements that were first discovered in the 3'UTR of mammalian transcripts. Over the past years, we compiled a series of ARE databases that revealed the extent and wide distribution of ARE-containing genes. For this update, we adopted an optimized search algorithm with improved specificity and sensitivity in ARE selection. The designation of the different ARE clusters was simplified by directly correlating the number of the ARE cluster to the number of overlapping AUUUA pentamers. Additionally, the new database was expanded to include genes with intronic AREs (pre-mRNAs) and their characteristics since recent observations reported their abundance and biological significance. Several enhancements were incorporated such as customized column view, additional search options and live search functionalities. The new version includes links to AREsite and AREScore, two related ARE assessment algorithms for further evaluation of the ARE characteristics. ARED-Plus now contains an updated repertoire of AREs in the human transcriptome that may be useful in several research fields.