DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions

By Dimitra Karagkouni, Maria D. Paraskevopoulou, Serafeim Chatzopoulos, Ioannis S. Vlachos, Spyros Tastsoglou, Ilias Kanellos, Dimitris Papadimitriou, Ioannis Kavakiotis, Sofia Maniou, G. Skoufos and 3 more. Nucleic Acids Res., 2017

965 citations recorded by the source corpus.

Abstract DIANA-TarBase v8 (http://www.microrna.gr/tarbase) is a reference database devoted to the indexing of experimentally supported microRNA (miRNA) targets. Its eighth version is the first database indexing >1 million entries, corresponding to ∼670 000 unique miRNA-target pairs. The interactions are supported by >33 experimental methodologies, applied to ∼600 cell types/tissues under ∼451 experimental conditions. It integrates information on cell-type specific miRNA–gene regulation, while hundreds of thousands of miRNA-binding locations are reported. TarBase is coming of age, with more than a decade of continuous support in the non-coding RNA field. A new module has been implemented that enables the browsing of interactions through different filtering combinations. It permits easy retrieval of positive and negative miRNA targets per species, methodology, cell type and tissue. An incorporated ranking system is utilized for the display of interactions based on the robustness of their supporting methodologies. Statistics, pie-charts and interactive bar-plots depicting the database content are available through a dedicated result page. An intuitive interface is introduced, providing a user-friendly application with flexible options to different queries.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c191684cfccc675c3bdca83aa5485dfc64c0d169

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Citations in the corpus

miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology (2020, methodology): “We have updated the miRNA interaction knowledgebase based on the latest releases from major miRNA annotation databases including miRBase (24), miRTarBase (25), TarBase (26), HMDD (27) etc.”
miRBase: from microRNA sequences to function (2018, background): “The TarBase (17) and miRTarBase (18) databases curate and provide lists of microRNA targets that have some experimental support.”
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases (2020, background): “In addition to sequences, RNAcentral provides a wide range of annotation types, such as genome coordinates, microRNA–target interactions (2,3), Gene Ontology (GO) terms (4), orthologs and paralogs (5), RNA family classification from Rfam (6) and more.”
Ensembl 2021 (2020, methodology): “This year, we incorporated updated enhancer activity data from VISTA (22) and miRNA/gene interactions from Tarbase v8 (23).”
NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis (2019, methodology): “TarBase (19) and miRTarbase (20) have been used to obtain experimentally validated miRNA–gene target information, while ENCODE (21), JASPAR (22) and CHEA (23) have been used to obtain TF–gene target Users can double click a meta-node (large semi-transparent circles) to view all its associated genes…”
RNAcentral: a hub of information for non-coding RNA sequences (2018, positive): “Additionally, we have imported ncRNA data from Ensembl (6), GENCODE (17), HGNC (HUGO Gene Nomenclature Committee) (18), and TarBase (19).”