TarBase-v9.0 extends experimentally supported miRNA–gene interactions to cell-types and virally encoded miRNAs

• Published in: Nucleic acids research 2024-01, Vol.52 (D1), p.D304-D310
• Main Authors: Skoufos, Giorgos, Kakoulidis, Panos, Tastsoglou, Spyros, Zacharopoulou, Elissavet, Kotsira, Vasiliki, Miliotis, Marios, Mavromati, Galatea, Grigoriadis, Dimitris, Zioga, Maria, Velli, Angeliki, Koutou, Ioanna, Karagkouni, Dimitra, Stavropoulos, Steve, Kardaras, Filippos S, Lifousi, Anna, Vavalou, Eustathia, Ovsepian, Armen, Skoulakis, Anargyros, Tasoulis, Sotiris K, Georgakopoulos, Spiros V, Plagianakos, Vassilis P, Hatzigeorgiou, Artemis G
• Format: Article
• Language: English
• Subjects: Animals; Databases, Nucleic Acid; Genes, Viral - genetics; Internet; MicroRNAs - genetics; MicroRNAs - metabolism
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkad1071

Abstract TarBase is a reference database dedicated to produce, curate and deliver high quality experimentally-supported microRNA (miRNA) targets on protein-coding transcripts. In its latest version (v9.0, https://dianalab.e-ce.uth.gr/tarbasev9), it pushes the envelope by introducing virally-encoded miRNAs, interactions leading to target-directed miRNA degradation (TDMD) events and the largest collection of miRNA–gene interactions to date in a plethora of experimental settings, tissues and cell-types. It catalogues ∼6 million entries, comprising ∼2 million unique miRNA–gene pairs, supported by 37 experimental (high- and low-yield) protocols in 172 tissues and cell-types. Interactions are annotated with rich metadata including information on genes/transcripts, miRNAs, samples, experimental contexts and publications, while millions of miRNA-binding locations are also provided at cell-type resolution. A completely re-designed interface with state-of-the-art web technologies, incorporates more features, and allows flexible and ingenious use. The new interface provides the capability to design sophisticated queries with numerous filtering criteria including cell lines, experimental conditions, cell types, experimental methods, species and/or tissues of interest. Additionally, a plethora of fine-tuning capacities have been integrated to the platform, offering the refinement of the returned interactions based on miRNA confidence and expression levels, while boundless local retrieval of the offered interactions and metadata is enabled. Graphical Abstract Graphical Abstract