The database of experimentally supported targets: a functional update of TarBase

By Giorgos L. Papadopoulos, Martin Reczko, Victor A. Simossis, Praveen Sethupathy, Artemis G. Hatzigeorgiou. Nucleic Acids Res., 2008

437 citations recorded by the source corpus.

TarBase5.0 is a database which houses a manually curated collection of experimentally supported microRNA (miRNA) targets in several animal species of central scientific interest, plants and viruses. MiRNAs are small non-coding RNA molecules that exhibit an inhibitory effect on gene expression, interfering with the stability and translational efficiency of the targeted mature messenger RNAs. Even though several computational programs exist to predict miRNA targets, there is a need for a comprehensive collection and description of miRNA targets with experimental support. Here we introduce a substantially extended version of this resource. The current version includes more than 1300 experimentally supported targets. Each target site is described by the miRNA that binds it, the gene in which it occurs, the nature of the experiments that were conducted to test it, the sufficiency of the site to induce translational repression and/or cleavage, and the paper from which all these data were extracted. Additionally, the database is functionally linked to several other relevant and useful databases such as Ensembl, Hugo, UCSC and SwissProt. The TarBase5.0 database can be queried or downloaded from http://microrna.gr/tarbase.

Subfields: Cancer Research, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/7b350770e051108a7b673a89c63ac43d4c4961f0

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Citations in the corpus

miRWalk - Database: Prediction of possible miRNA binding sites by "walking" the genes of three genomes (2011, neutral): “0) [42], miRecords (version 3) [21] and miRTarBase (release 2.”
miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets (2012, methodology): “Seven algorithms predicting miRNA targets, DIANA-microT [13] [14], miRanda [9] [22] [23], mirBridge [15], PicTar [16], PITA [18] , rna22 [17] , and TargetScan [10] [11] [12], and two experimentally validated databases, TarBase [24] and miRecords [25], of miRNA target genes were included.”
TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support (2011, background): “TarBase 5.0 DIANA Lab’s TarBase (17) was ﬁrst released in 2005 and its ﬁfth version includes 1300 experimentally supported targets from eight species that were manually curated from relevant literature.”
miRTarBase: a database curates experimentally validated microRNA–target interactions (2010, background): “TarBase is the ﬁrst resource to provide experimentally veriﬁed MTIs by surveying pertinent literature (9). miRecords accumulates both experimentally validated miRNA targets and computationally predicted miRNA targets (10). miR2Disease contains relationships among miRNAs, target genes and diseases…”
starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data (2010, background): “In addition, several resources have been established to systematically collect and describe both experimentally validated miRNA targets [TarBase (13), miRecords (14)] and predicted miRNA targets [miRGator (15), MiRNAMap (16)].”
DIANA-microT web server: elucidating microRNA functions through target prediction (2009, neutral): “Cases where an interaction is registered in the database of experimentally supported miRNA targets [TarBase, (8)] are high-lighted with a link to the database.”
An overview of microRNAs (2015, background): “In the case of MCM7 there are three clustered miRNA stem loops, each leading to a distinct mature miRNA with a unique target set[21].”
miRBase: integrating microRNA annotation and deep-sequencing data (2010, background): “org (22)], together with lists of validated microRNA target sites [currently curated by resources such as TarBase (23), miRecords (24), miRTarBase].”