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

被引：31

作者：

Skoufos, Giorgos ^{[1
,2
]}

Kakoulidis, Panos ^{[3
,4
]}

Tastsoglou, Spyros ^{[1
,2
]}

Zacharopoulou, Elissavet ^{[1
,2
]}

Kotsira, Vasiliki ^{[1
,2
]}

Miliotis, Marios ^{[1
,2
]}

Mavromati, Galatea ^{[1
]}

Grigoriadis, Dimitris ^{[1
]}

Zioga, Maria ^{[1
]}

Velli, Angeliki ^{[1
]}

Koutou, Ioanna ^{[1
]}

Karagkouni, Dimitra ^{[1
,2
,9
,10
]}

Stavropoulos, Steve ^{[5
]}

Kardaras, Filippos S. ^{[1
,2
]}

Lifousi, Anna ^{[6
]}

Vavalou, Eustathia ^{[7
]}

Ovsepian, Armen ^{[1
,2
]}

Skoulakis, Anargyros ^{[1
,2
]}

Tasoulis, Sotiris K. ^{[5
]}

Georgakopoulos, Spiros, V ^{[8
]}

Plagianakos, Vassilis P. ^{[5
]}

Hatzigeorgiou, Artemis G. ^{[1
,2
]}

机构：

[1] Univ Thessaly, Dept Comp Sci & Biomed Informat, DIANA Lab, Lamia, Greece

[2] Hellenic Pasteur Inst, Athens 11521, Greece

[3] Natl & Kapodistrian Univ Athens, Dept Informat & Telecommun, Athens, Greece

[4] Acad Athens, Biomed Res Fdn, Athens 11527, Greece

[5] Univ Thessaly, Dept Comp Sci & Biomed Informat, Lamia, Greece

[6] Tech Univ Denmark, Dept Hlth Technol, Lyngby, Denmark

[7] Natl & Kapodistrian Univ Athens, Dept Biol, Athens 15784, Greece

[8] Univ Thessaly, Dept Math, Lamia, Greece

[9] Harvard Med Sch, Canc Res Inst, Beth Israel Deaconess Med Ctr, Dept Pathol, Boston, MA USA

[10] Harvard Med Sch, Boston, MA USA

来源：

NUCLEIC ACIDS RESEARCH | 2023年 / 52卷 / D1期

关键词：

MICRORNAS; NETWORKS; PROTEIN;

D O I：

10.1093/nar/gkad1071

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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

引用

页码：D304 / D310

页数：7

共 42 条

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