Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://www.microrna.gr/LncBase
Full name: Database on miRNA-lncRNA interactions
Description: LncBase hosts elaborated information for,both predicted and experimentally verified,miRNA-lncRNA interactions. The database consists of two distinct modules.
Year founded: 2012
Last update: 2015-11-26
Version: v2.0
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: Greece
Data type:
RNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: University of Thessaly
Address: DIANA-Lab, Department of Computer & Communication Engineering, University of Thessaly, 382 21, Volos, Greece
City: Athens
Province/State:
Country/Region: Greece
Contact name (PI/Team): Artemis G. Hatzigeorgiou
Contact email (PI/Helpdesk): arhatzig@inf.uth.gr

Publications

26612864
DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. [PMID: 26612864]
Paraskevopoulou MD, Vlachos IS, Karagkouni D, Georgakilas G, Kanellos I, Vergoulis T, Zagganas K, Tsanakas P, Floros E, Dalamagas T, Hatzigeorgiou AG.

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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2016:44(D1) | 253 Citations (from Europe PMC, 2022-01-15)
23193281
DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. [PMID: 23193281]
Paraskevopoulou MD, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas TM, Hatzigeorgiou AG.

Recently, the attention of the research community has been focused on long non-coding RNAs (lncRNAs) and their physiological/pathological implications. As the number of experiments increase in a rapid rate and transcriptional units are better annotated, databases indexing lncRNA properties and function gradually become essential tools to this process. Aim of DIANA-LncBase (www.microrna.gr/LncBase) is to reinforce researchers' attempts and unravel microRNA (miRNA)-lncRNA putative functional interactions. This study provides, for the first time, a comprehensive annotation of miRNA targets on lncRNAs. DIANA-LncBase hosts transcriptome-wide experimentally verified and computationally predicted miRNA recognition elements (MREs) on human and mouse lncRNAs. The analysis performed includes an integration of most of the available lncRNA resources, relevant high-throughput HITS-CLIP and PAR-CLIP experimental data as well as state-of-the-art in silico target predictions. The experimentally supported entries available in DIANA-LncBase correspond to >5000 interactions, while the computationally predicted interactions exceed 10 million. DIANA-LncBase hosts detailed information for each miRNA-lncRNA pair, such as external links, graphic plots of transcripts' genomic location, representation of the binding sites, lncRNA tissue expression as well as MREs conservation and prediction scores.

Nucleic Acids Res. 2013:41(Database issue) | 209 Citations (from Europe PMC, 2022-01-15)

Ranking

All databases:
185/5050 (96.356%)
Interaction:
28/779 (96.534%)
185
Total Rank
462
Citations
51.333
z-index

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Word cloud

Record metadata

Created on: 2015-06-20
Curated by:
Lina Ma [2016-05-30]
Lina Ma [2016-04-07]
Jian Sang [2016-04-04]
lin liu [2016-02-08]
lin liu [2016-01-29]
Zhang Zhang [2016-01-06]
lin liu [2016-01-01]
Jian Sang [2015-12-07]
Lina Ma [2015-11-10]
Jian Sang [2015-06-26]