DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs

By Maria D. Paraskevopoulou, G. Georgakilas, Nikos Kostoulas, Martin Reczko, Manolis Maragkakis, Theodore Dalamagas, Artemis G. Hatzigeorgiou. Nucleic Acids Res., 2012

342 citations recorded by the source corpus.

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.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/222dba366d02dd5fc1dbf691da2a98b0e5b796a7

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Citations in the corpus

DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions (2014, neutral): “0 (28), microT-CDS (29) and LncBase (30), respectively.”
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database (2015, methodology): “The DIANA-LncBase (18) is a database of miRNA-lncRNA-putative functional interactions and provides comprehensive annotations of miRNA targets on lncRNAs. miRGate (19) contains novel computationally predicted miRNA–mRNA pairs as well as experimentally validated data from four well known databases.”
NONCODEv4: exploring the world of long non-coding RNA genes (2013, background): “NONCODE has already proven to be an important resource in the realm of ncRNA databases, and is therefore incorporated into other ncRNA databases such as fRNAdb — a large collection of ncRNAs (16), GeneCards — the comprehensive human gene compendium (17) and DIANA-LncBase — a database for miRNAs targ”
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs (2014, methodology): “For example, algorithms for finding microRNAs targeting lncRNAs can be accessed at DIANA-LncBase (9) and starBase v2.”
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data (2013, methodology): “We and others have used CLIP-seq data generated from HEK293 cells to characterize miRNA-mRNA and miRNA-lncRNA interactions (17–21).”
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions (2013, background): “DIANA-LncBase (25) provides comprehensive annotations of miRNA targets on long non-coding RNAs with transcriptome-wide experimentally verified and computationally predicted miRNA recognition elements.”
Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers (2015, neutral): “DIANA-LncBase (13) identifies miRNA– lncRNA interactions.”