DIANA-LncBase v2 – indexing microRNA targets on non-coding transcripts

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 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.

rna-seq

Snapshot depicting the DIANA-LncBase v2 interface. Queries using one or more microRNAs and/or lncRNAs [1] or even the coordinates of a genomic location [2] are supported. Users can add and remove search terms or filter [3] their results based on cell/tissue type and experimental methodology, as well as the experimental outcome (positive/negative) or type of validation (direct/indirect). LncBase offers extensive information for each identified interaction, such as gene/miRNA details [4,5], as well as active links to UCSC graphical representation [6], Ensembl, miRBase and DIANA disease tag cloud [8]. LncBase also provides useful information for each performed experiment [9], including the methodology, cell or tissue that was utilized, as well as a link to the original publication. There are direct links to external applications such as microT, TarBase, miRPath, where the studied miRNA can be further examined. Interactions are also coupled with miRNA binding site details [10]. Users can navigate between the Experimental and Predicted LncBase v2 modules [11]. The Help button [12] leads to the LncBase Help section.

Availability – the DIANA-LncBase v2 is available at: http://www.microrna.gr/LncBase

Paraskevopoulou MD, Vlachos IS, Karagkouni D, Georgakilas G, Kanellos I, Vergoulis T, Zagganas K, Tsanakas P, Floros E, Dalamagas T, Hatzigeorgiou AG. (2015) DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Nucleic Acids Res [Epub ahead of print]. [article]

Leave a Reply

Your email address will not be published. Required fields are marked *

*

Time limit is exhausted. Please reload CAPTCHA.