DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts
DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts
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DOI：
10.1093/nar/gkz1036
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发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
Hatzigeorgiou, Artemis G.
中科院分区：
文献类型：
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作者：
Karagkouni, Dimitra;Paraskevopoulou, Maria D.;Hatzigeorgiou, Artemis G.
diana - lnbase v3.0 （www.microrna.gr/LncBase）是一个参考库，实验支持非编码转录物上的miRNA靶点。它的第三个版本提供了大约50万个条目，对应于大约24万个独特的组织和细胞类型特异性miRNA-lncRNA对。这种交互的汇编来源于出版物的手动管理和bbb300高通量数据集的分析。miRNA靶点由14种实验方法支持，适用于人和小鼠243种不同的细胞类型和组织。数据库中最大的部分是高度可信的ago - clip衍生的mirna结合事件。lnbase v3.0是第一个采用强大的clip - seq引导算法（microCLIP框架）的相关数据库，可分析236个AGO-CLIP-Seq库并编目37万个类似的miRNA结合事件。数据库从头开始重新设计，提供了新的功能。已知的短变异信息，在bbb67,000实验支持的靶点和不同细胞区室的lncRNA表达谱迎合用户。交互式可视化图，描绘了miRNA-lncRNA对的相关性，以及lncRNA在广泛的细胞类型和组织中的表达谱，首次通过专门的页面呈现。lnbase v3.0为ncRNA研究提供了宝贵的资源，为理解仍未被广泛探索的lncRNA功能提供了新的见解。
DIANA-LncBase v3.0 (www.microrna.gr/LncBase) is a reference repository with experimentally supported miRNA targets on non-coding transcripts. Its third version provides approximately half a million entries, corresponding to similar to 240 000 unique tissue and cell type specific miRNA-lncRNA pairs. This compilation of interactions is derived from the manual curation of publications and the analysis of >300 high-throughput datasets. miRNA targets are supported by 14 experimental methodologies, applied to 243 distinct cell types and tissues in human and mouse. The largest part of the database is highly confident, AGO-CLIP-derived miRNA-binding events. LncBase v3.0 is the first relevant database to employ a robust CLIP-Seq-guided algorithm, microCLIP framework, to analyze 236 AGO-CLIP-Seq libraries and catalogue similar to 370 000 miRNA binding events. The database was redesigned from the ground up, providing new functionalities. Known short variant information, on >67,000 experimentally supported target sites and lncRNA expression profiles in different cellular compartments are catered to users. Interactive visualization plots, portraying correlations of miRNA-lncRNA pairs, as well as lncRNA expression profiles in a wide range of cell types and tissues, are presented for the first time through a dedicated page. LncBase v3.0 constitutes a valuable asset for ncRNA research, providing new insights to the understanding of the still widely unexplored lncRNA functions.