Format

Send to

Choose Destination
Nucleic Acids Res. 2019 Nov 16. pii: gkz1036. doi: 10.1093/nar/gkz1036. [Epub ahead of print]

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

Author information

1
DIANA-Lab, Department of Electrical and Computer Engineering, Univ. of Thessaly, 38221 Volos, Greece.
2
Hellenic Pasteur Institute, 11521 Athens, Greece.
3
Department of Computer Science and Biomedical Informatics, Univ. of Thessaly, 351 31 Lamia, Greece.
4
Department of Informatics and Telecommunications, Postgraduate Program: 'Information Technologies in Medicine and Biology', University of Athens, 15784 Athens, Greece.

Abstract

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 ∼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 ∼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.

PMID:
31732741
DOI:
10.1093/nar/gkz1036

Supplemental Content

Full text links

Icon for Silverchair Information Systems
Loading ...
Support Center