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

By Thanasis Vergoulis, Ioannis S. Vlachos, Panagiotis Alexiou, G. Georgakilas, Manolis Maragkakis, Martin Reczko, Stefanos Gerangelos, N. Koziris, Theodore Dalamagas, Artemis G. Hatzigeorgiou. Nucleic Acids Res., 2011

586 citations recorded by the source corpus.

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.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6bdd6008f12ecb99faf9ebcce2dcde1663f8a919

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Citations in the corpus

Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, methodology): “Experimentally validated microRNA–mRNA interactions are available from TarBase (Vergoulis et al., 2012), while predicted interactions can be accessed at TargetScan and PicTar (Krek et al., 2005; Lewis et al., 2005).”
miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis (2016, methodology): “To manage the growing datasets, many online databases have been developed such as TarBase (12), miRTarBase”
HMDD v3.0: a database for experimentally supported human microRNA–disease associations (2018, methodology): “Besides, we added the regulation pattern (up/down) between miRNA and genes, using the annotations from TarBase v8 (24).”
DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways (2012, background): “0 database (12) is also incorporated into the new schema.”
Identifying miRNAs, targets and functions (2012, background): “While some validated miRNAs and their target genes have been collated in databases, such as TarBase [100] and miRecords [75], these in no way reflect the diversity and abundance of potential miRNA regulatory influences.”
DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions (2014, background): “The first high-throughput techniques that became available could be considered as an increased throughput/lower accuracy version of specific techniques (8).”
MicroRNAs and complex diseases: from experimental results to computational models (2019, unknown): “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.”
The Emerging Paradigm of Network Medicine in the Study of Human Disease (2012, background): “26 In concert, high-throughput analyses using transcriptional expression arrays and/or proteomics have allowed for verification and identification of additional miRNA targets, 27 which have been incorporated into a number of these databases (eg, DIANA and TarBase 28 ).”
DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows (2013, background): “0 (3) or/and predicted interactions from microT-CDS.”
Ensembl 2015 (2014, methodology): “We store external annotations, such as the VISTA enhancers, the FANTOM5 promoters (17) and enhancers (18) and the Diana TarBase miRNA target predictions (19).”
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions (2013, background): “TarBase (21) contains a manually curated collection of experimentally tested miRNA targets, in humans, mice, fruit flies, worms and zebrafish.”
The multiMiR R package and database: integration of microRNA–target interactions along with their disease and drug associations (2014, methodology): “6) is another Bioconductor package which includes predictions from five programs (MicroCosm, miRanda (7), miRDB (13), PicTar (6) and TargetScan) and validations from TarBase (26) in human.”
Ensembl regulation resources (2016, background): “These include: a set of human and mouse miRNA target predictions provided by DIANA-TarBase (42), experimentally validated non-coding regions from the VISTA enhancer browser (43), and regions highlighted by the FANTOM 5 project (44, 45).”