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Nucleic Acids Res. 2016 Jan 4;44(D1):D231-8. doi: 10.1093/nar/gkv1270. Epub 2015 Nov 26.

DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts.

Author information

1
DIANA-Lab, Department of Computer & Communication Engineering, University of Thessaly, 382 21, Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece mparaskevopoulou@inf.uth.gr.
2
DIANA-Lab, Department of Computer & Communication Engineering, University of Thessaly, 382 21, Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece Laboratory for Experimental Surgery and Surgical Research 'N.S. Christeas', Medical School of Athens, University of Athens, 11527, Greece.
3
DIANA-Lab, Department of Computer & Communication Engineering, University of Thessaly, 382 21, Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece.
4
'Athena' Research and Innovation Center, 11524, Athens, Greece University of Peloponnisos, Department of Informatics and Telecommunications, 22100, Tripoli, Greece.
5
'Athena' Research and Innovation Center, 11524, Athens, Greece.
6
'Athena' Research and Innovation Center, 11524, Athens, Greece School of Electrical and Computer Engineering, NTUA, 15773 Zografou, Greece.
7
University of Peloponnisos, Department of Informatics and Telecommunications, 22100, Tripoli, Greece Greek Research and Technology Network (GRNET), Athens 11527, Greece.
8
Greek Research and Technology Network (GRNET), Athens 11527, Greece.
9
'Athena' Research and Innovation Center, 11524, Athens, Greece dalamag@imis.athena-innovation.gr.
10
DIANA-Lab, Department of Computer & Communication Engineering, University of Thessaly, 382 21, Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece 'Athena' Research and Innovation Center, 11524, Athens, Greece arhatzig@inf.uth.gr.

Abstract

microRNAs (miRNAs) are short non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of coding gene expression. Long non-coding RNAs (lncRNAs) have been recently reported to interact with miRNAs. The sponge-like function of lncRNAs introduces an extra layer of complexity in the miRNA interactome. DIANA-LncBase v1 provided a database of experimentally supported and in silico predicted miRNA Recognition Elements (MREs) on lncRNAs. The second version of LncBase (www.microrna.gr/LncBase) presents an extensive collection of miRNA:lncRNA interactions. The significantly enhanced database includes more than 70 000 low and high-throughput, (in)direct miRNA:lncRNA experimentally supported interactions, derived from manually curated publications and the analysis of 153 AGO CLIP-Seq libraries. The new experimental module presents a 14-fold increase compared to the previous release. LncBase v2 hosts in silico predicted miRNA targets on lncRNAs, identified with the DIANA-microT algorithm. The relevant module provides millions of predicted miRNA binding sites, accompanied with detailed metadata and MRE conservation metrics. LncBase v2 caters information regarding cell type specific miRNA:lncRNA regulation and enables users to easily identify interactions in 66 different cell types, spanning 36 tissues for human and mouse. Database entries are also supported by accurate lncRNA expression information, derived from the analysis of more than 6 billion RNA-Seq reads.

PMID:
26612864
PMCID:
PMC4702897
DOI:
10.1093/nar/gkv1270
[Indexed for MEDLINE]
Free PMC Article

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