DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions

By Ioannis S. Vlachos, Maria D. Paraskevopoulou, Dimitra Karagkouni, G. Georgakilas, Thanasis Vergoulis, Ilias Kanellos, I. Anastasopoulos, Sofia Maniou, K. Karathanou, Despina Kalfakakou and 3 more. Nucleic Acids Res., 2014

755 citations recorded by the source corpus.

microRNAs (miRNAs) are short non-coding RNA species, which act as potent gene expression regulators. Accurate identification of miRNA targets is crucial to understanding their function. Currently, hundreds of thousands of miRNA:gene interactions have been experimentally identified. However, this wealth of information is fragmented and hidden in thousands of manuscripts and raw next-generation sequencing data sets. DIANA-TarBase was initially released in 2006 and it was the first database aiming to catalog published experimentally validated miRNA:gene interactions. DIANA-TarBase v7.0 (http://www.microrna.gr/tarbase) aims to provide for the first time hundreds of thousands of high-quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data. DIANA-TarBase v7.0 enables users to easily identify positive or negative experimental results, the utilized experimental methodology, experimental conditions including cell/tissue type and treatment. The new interface provides also advanced information ranging from the binding site location, as identified experimentally as well as in silico, to the primer sequences used for cloning experiments. More than half a million miRNA:gene interactions have been curated from published experiments on 356 different cell types from 24 species, corresponding to 9- to 250-fold more entries than any other relevant database. DIANA-TarBase v7.0 is freely available.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a23bb84bc4eb3ff5a7625aa86f02c2e4a5f9dfb7

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Citations in the corpus

MicroRNAs and complex diseases: from experimental results to computational models (2019, neutral): “gr/tarbase) [182, 183] TarBase is a comprehensive database of animal miRNA targets, whose current version indexes more than half a million experimentally validated miRNA–gene interactions covering 356 distinct cell types from 24 species.”
DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions (2017, methodology): “This extension provides an increase of ∼200 000 interactions and ∼300 000 entries since the previous version (8).”
miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions (2021, methodology): “DIANA-TarBase includes manually curated interactions between miRNAs and genes through detailed metadata, experimental methods and conditional annotations (9).”
mirDIP 4.1—integrative database of human microRNA target predictions (2017, background): “CUDA-miRanda 2014 yes yes yes (28) Cupid 2011 2015 yes yes yes (29) DIANA 2012 yes yes yes yes yes yes yes (30)”
TransmiR v2.0: an updated transcription factor-microRNA regulation database (2018, positive): “Finally, experimentally validated miRNA-TF feedback regulations derived from miRNA target databases (TarBase (26) and miRTarBase (27)) were also included in TransmiR v2.”
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database (2015, methodology): “DIANA-TarBase (13), similar to our database hosts detailed information concerning each miRNA-gene interaction, ranging from miRNA-and gene-related facts to information that are specific to their interactions, experimental validation methodologies and their outcomes.”
Tools for Sequence-Based miRNA Target Prediction: What to Choose? (2016, background): “, containing only information about validated miRNAs, as is the case with TarBase [46].”
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions (2017, neutral): “The DIANA-TarBase (6) is a database that contains manually curated experimentally validated miRNA-gene interactions, with detailed meta-data, experimental methodologies, and conditions.”
miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database (2019, methodology): “DIANA-TarBase accumulates manually curated interactions between miRNA and gene with the annotations of detailed meta-data, experimental methodologies and conditions (8).”