RISE: a database of RNA interactome from sequencing experiments.
RISE: a database of RNA interactome from sequencing experiments.
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RISE：测序实验中的 RNA 相互作用组数据库
DOI：
10.1093/nar/gkx864
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Zhang QC
中科院分区：
文献类型：
--
作者：
Gong J;Shao D;Xu K;Lu Z;Lu ZJ;Yang YT;Zhang QC
摘要我们介绍了RISE(http://rise.zhanglab.net)，)，这是一个来自测序实验的RNA相互作用组数据库。RNA-RNA相互作用(RRIs)是RNA调节和功能所必需的。Rise提供了一个全面的RRIs集合，主要来自最近基于转录组范围的测序实验，如Paris、Splash、LIGR-seq和Mario，以及目标研究，如RIA-seq、RAP-RNA和Clash。它还包括从其他主要数据库和出版物汇总的互动。RISE数据库目前包含328,811个RNA-RNA相互作用，主要在人类、小鼠和酵母中。虽然大多数现有的RNA数据库主要包含miRNA靶向的相互作用，但值得注意的是，RISE中超过一半的RRIs位于mRNA和长非编码RNA之间。我们比较了RISE中不同的RRI数据集，发现通过不同技术和不同细胞系解决的相互作用中存在有限的重叠。它可能会暗示技术偏好，也可能暗示区域创新机构的动态性质。我们还分析了人类和小鼠RRI网络的基本特征，发现它们倾向于无标度、小世界、层次化和模块化。该分析可能会提名重要的RNAs或RRIs进行进一步研究。最后，RISE提供了Circos图和几个用于综合可视化的表视图，并带有广泛的分子和功能注释，以便于探索任何感兴趣的RRI的生物学功能。
Abstract We present RISE (http://rise.zhanglab.net), a database of RNA Interactome from Sequencing Experiments. RNA-RNA interactions (RRIs) are essential for RNA regulation and function. RISE provides a comprehensive collection of RRIs that mainly come from recent transcriptome-wide sequencing-based experiments like PARIS, SPLASH, LIGR-seq, and MARIO, as well as targeted studies like RIA-seq, RAP-RNA and CLASH. It also includes interactions aggregated from other primary databases and publications. The RISE database currently contains 328,811 RNA-RNA interactions mainly in human, mouse and yeast. While most existing RNA databases mainly contain interactions of miRNA targeting, notably, more than half of the RRIs in RISE are among mRNA and long non-coding RNAs. We compared different RRI datasets in RISE and found limited overlaps in interactions resolved by different techniques and in different cell lines. It may suggest technology preference and also dynamic natures of RRIs. We also analyzed the basic features of the human and mouse RRI networks and found that they tend to be scale-free, small-world, hierarchical and modular. The analysis may nominate important RNAs or RRIs for further investigation. Finally, RISE provides a Circos plot and several table views for integrative visualization, with extensive molecular and functional annotations to facilitate exploration of biological functions for any RRI of interest.
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影响因子：
10.5
作者：
Cabili, Moran N.;Trapnell, Cole;Rinn, John L.
通讯作者：
Rinn, John L.
影响因子：
64.5
作者：
Helwak A;Kudla G;Dudnakova T;Tollervey D
通讯作者：
Tollervey D
DOI：
10.1093/database/baw167
发表时间：
2017
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Junge A;Refsgaard JC;Garde C;Pan X;Santos A;Alkan F;Anthon C;von Mering C;Workman CT;Jensen LJ;Gorodkin J
通讯作者：
Gorodkin J
影响因子：
64.5
作者：
Lu Z;Zhang QC;Lee B;Flynn RA;Smith MA;Robinson JT;Davidovich C;Gooding AR;Goodrich KJ;Mattick JS;Mesirov JP;Cech TR;Chang HY
通讯作者：
Chang HY
影响因子：
64.5
作者：
Engreitz JM;Sirokman K;McDonel P;Shishkin AA;Surka C;Russell P;Grossman SR;Chow AY;Guttman M;Lander ES
通讯作者：
Lander ES