DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts

被引：244

作者：

Karagkouni, Dimitra ^{[1
,2
,3
]}

Paraskevopoulou, Maria D. ^{[1
,2
]}

Tastsoglou, Spyros ^{[1
,2
]}

Skoufos, Giorgos ^{[1
,2
]}

Karavangeli, Anna ^{[1
,3
]}

Pierros, Vasilis ^{[1
,2
]}

Zacharopoulou, Elissavet ^{[1
,4
]}

Hatzigeorgiou, Artemis G. ^{[1
,2
,3
]}

机构：

[1] Univ Thessaly, Dept Elect & Comp Engn, DIANA Lab, Volos 38221, Greece

[2] Hellenic Pasteur Inst, Athens 11521, Greece

[3] Univ Thessaly, Dept Comp Sci & Biomed Informat, Lamia 35131, Greece

[4] Univ Athens, Dept Informat & Telecommun, Postgrad Program Informat Technol Med & Biol, Athens 15784, Greece

来源：

NUCLEIC ACIDS RESEARCH | 2020年 / 48卷 / D1期

关键词：

RNA; DATABASE; IDENTIFICATION; EXPRESSION;

D O I：

10.1093/nar/gkz1036

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：D101 / D110

页数：10

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