TY - JOUR
T1 - TarBase-v9.0 extends experimentally supported miRNA-gene interactions to cell-types and virally encoded miRNAs
AU - Skoufos, Giorgos
AU - Kakoulidis, Panos
AU - Tastsoglou, Spyros
AU - Zacharopoulou, Elissavet
AU - Kotsira, Vasiliki
AU - Miliotis, Marios
AU - Mavromati, Galatea
AU - Grigoriadis, Dimitris
AU - Zioga, Maria
AU - Velli, Angeliki
AU - Koutou, Ioanna
AU - Karagkouni, Dimitra
AU - Stavropoulos, Steve
AU - Kardaras, Filippos S.
AU - Lifousi, Anna
AU - Vavalou, Eustathia
AU - Ovsepian, Armen
AU - Skoulakis, Anargyros
AU - Tasoulis, Sotiris K.
AU - Georgakopoulos, Spiros
AU - Plagianakos, Vassilis P.
AU - Hatzigeorgiou, Artemis G.
PY - 2023
Y1 - 2023
N2 - 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 similar to 6 million entries, comprising similar to 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
AB - 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 similar to 6 million entries, comprising similar to 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
KW - Databases, Nucleic Acid
KW - MicroRNAs
U2 - 10.1093/nar/gkad1071
DO - 10.1093/nar/gkad1071
M3 - Journal article
C2 - 37986224
SN - 0305-1048
VL - 52
SP - D304-D310
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -