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. 2012 Jan;40(Database issue):D222-9.
doi: 10.1093/nar/gkr1161. Epub 2011 Dec 1.

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

Thanasis Vergoulis  1 , Ioannis S Vlachos, Panagiotis Alexiou, George Georgakilas, Manolis Maragkakis, Martin Reczko, Stefanos Gerangelos, Nectarios Koziris, Theodore Dalamagas, Artemis G Hatzigeorgiou
Affiliations

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

Thanasis Vergoulis et al. Nucleic Acids Res. 2012 Jan.

Abstract

As the relevant literature and the number of experiments increase at a super linear rate, databases that curate and collect experimentally verified microRNA (miRNA) targets have gradually emerged. These databases attempt to provide efficient access to this wealth of experimental data, which is scattered in thousands of manuscripts. Aim of TarBase 6.0 (http://www.microrna.gr/tarbase) is to face this challenge by providing a significant increase of available miRNA targets derived from all contemporary experimental techniques (gene specific and high-throughput), while incorporating a powerful set of tools in a user-friendly interface. TarBase 6.0 hosts detailed information for each miRNA-gene interaction, ranging from miRNA- and gene-related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. All database entries are enriched with function-related data, as well as general information derived from external databases such as UniProt, Ensembl and RefSeq. DIANA microT miRNA target prediction scores and the relevant prediction details are available for each interaction. TarBase 6.0 hosts the largest collection of manually curated experimentally validated miRNA-gene interactions (more than 65,000 targets), presenting a 16.5-175-fold increase over other available manually curated databases.

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Figures

Figure 1.
Figure 1.
The annual growth of miRNA-related publications in PubMed and the number of entries in miRBase database.
Figure 2.
Figure 2.
The adopted text-mining-assisted curation pipeline.
Figure 3.
Figure 3.
Comparison of the number of targets per experimental validation method of TarBase 5.0 and TarBase 6.0. The number of targets is shown on a log2 scale (i.e. one visible unit represents twice the amount of available targets). Exponential increases thus appear as linear.
Figure 4.
Figure 4.
Screenshot of the TarBase 6.0 interface. The results of a query regarding mmu-miR-20a are depicted in the form of an expandable list. The miRNA details section is selected by the user for the first entry, showing details of supporting publications and validation experiments.
See this image and copyright information in PMC

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