MiRTarBase 2020: Updates to the experimentally validated microRNA-target interaction database

Hsi Yuan Huang; Yang Chi Dung Lin; Jing Li; Kai Yao Huang; Sirjana Shrestha; Hsiao Chin Hong; Yun Tang; Yi Gang Chen; Chen Nan Jin; Yuan Yu; Jia Tong Xu; Yue Ming Li; Xiao Xuan Cai; Zhen Yu Zhou; Xiao Hang Chen; Yuan Yuan Pei; Liang Hu; Jin Jiang Su; Shi Dong Cui; Fei Wang; Yue Yang Xie; Si Yuan Ding; Meng Fan Luo; Chih Hung Chou; Nai Wen Chang; Kai Wen Chen; Yu Hsiang Cheng; Xin Hong Wan; Wen Lian Hsu; Tzong Yi Lee; Feng Xiang Wei; Hsien Da Huang

doi:10.1093/nar/gkz896

MiRTarBase 2020: Updates to the experimentally validated microRNA-target interaction database

Hsi Yuan Huang, Yang Chi Dung Lin, Jing Li, Kai Yao Huang, Sirjana Shrestha, Hsiao Chin Hong, Yun Tang, Yi Gang Chen, Chen Nan Jin, Yuan Yu, Jia Tong Xu, Yue Ming Li, Xiao Xuan Cai, Zhen Yu Zhou, Xiao Hang Chen, Yuan Yuan Pei, Liang Hu, Jin Jiang Su, Shi Dong Cui, Fei WangYue Yang Xie, Si Yuan Ding, Meng Fan Luo, Chih Hung Chou, Nai Wen Chang, Kai Wen Chen, Yu Hsiang Cheng, Xin Hong Wan, Wen Lian Hsu, Tzong Yi Lee, Feng Xiang Wei, Hsien Da Huang

Research output: Journal Publication › Article › peer-review

399 Citations (Scopus)

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs (typically consisting of 18-25 nucleotides) that negatively control expression of target genes at the post-transcriptional level. Owing to the biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA-target interactions (MTIs). To date, the database has accumulated >13,404 validated MTIs from 11,021 articles from manual curations. In this update, a text-mining system was incorporated to enhance the recognition of MTI-related articles by adopting a scoring system. In addition, a variety of biological databases were integrated to provide information on the regulatory network of miRNAs and its expression in blood. Not only targets of miRNAs but also regulators of miRNAs are provided to users for investigating the up-and downstream regulations of miRNAs. Moreover, the number of MTIs with high-throughput experimental evidence increased remarkably (validated by CLIP-seq technology). In conclusion, these improvements promote the miRTarBase as one of the most comprehensively annotated and experimentally validated miRNA-target interaction databases. The updated version of miRTarBase is now available at http://miRTarBase.cuhk.edu.cn/.

Original language	English
Pages (from-to)	D148-D154
Journal	Nucleic Acids Research
Volume	48
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkz896
Publication status	Published - 1 Jan 2020
Externally published	Yes

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkz896

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Huang, H. Y., Lin, Y. C. D., Li, J., Huang, K. Y., Shrestha, S., Hong, H. C., Tang, Y., Chen, Y. G., Jin, C. N., Yu, Y., Xu, J. T., Li, Y. M., Cai, X. X., Zhou, Z. Y., Chen, X. H., Pei, Y. Y., Hu, L., Su, J. J., Cui, S. D., ... Huang, H. D. (2020). MiRTarBase 2020: Updates to the experimentally validated microRNA-target interaction database. Nucleic Acids Research, 48(D1), D148-D154. https://doi.org/10.1093/nar/gkz896

Huang, Hsi Yuan ; Lin, Yang Chi Dung ; Li, Jing ; Huang, Kai Yao ; Shrestha, Sirjana ; Hong, Hsiao Chin ; Tang, Yun ; Chen, Yi Gang ; Jin, Chen Nan ; Yu, Yuan ; Xu, Jia Tong ; Li, Yue Ming ; Cai, Xiao Xuan ; Zhou, Zhen Yu ; Chen, Xiao Hang ; Pei, Yuan Yuan ; Hu, Liang ; Su, Jin Jiang ; Cui, Shi Dong ; Wang, Fei ; Xie, Yue Yang ; Ding, Si Yuan ; Luo, Meng Fan ; Chou, Chih Hung ; Chang, Nai Wen ; Chen, Kai Wen ; Cheng, Yu Hsiang ; Wan, Xin Hong ; Hsu, Wen Lian ; Lee, Tzong Yi ; Wei, Feng Xiang ; Huang, Hsien Da. / MiRTarBase 2020 : Updates to the experimentally validated microRNA-target interaction database. In: Nucleic Acids Research. 2020 ; Vol. 48, No. D1. pp. D148-D154.

@article{6c93dedbb1854806bc37904d47342dda,

title = "MiRTarBase 2020: Updates to the experimentally validated microRNA-target interaction database",

abstract = "MicroRNAs (miRNAs) are small non-coding RNAs (typically consisting of 18-25 nucleotides) that negatively control expression of target genes at the post-transcriptional level. Owing to the biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA-target interactions (MTIs). To date, the database has accumulated >13,404 validated MTIs from 11,021 articles from manual curations. In this update, a text-mining system was incorporated to enhance the recognition of MTI-related articles by adopting a scoring system. In addition, a variety of biological databases were integrated to provide information on the regulatory network of miRNAs and its expression in blood. Not only targets of miRNAs but also regulators of miRNAs are provided to users for investigating the up-and downstream regulations of miRNAs. Moreover, the number of MTIs with high-throughput experimental evidence increased remarkably (validated by CLIP-seq technology). In conclusion, these improvements promote the miRTarBase as one of the most comprehensively annotated and experimentally validated miRNA-target interaction databases. The updated version of miRTarBase is now available at http://miRTarBase.cuhk.edu.cn/.",

author = "Huang, {Hsi Yuan} and Lin, {Yang Chi Dung} and Jing Li and Huang, {Kai Yao} and Sirjana Shrestha and Hong, {Hsiao Chin} and Yun Tang and Chen, {Yi Gang} and Jin, {Chen Nan} and Yuan Yu and Xu, {Jia Tong} and Li, {Yue Ming} and Cai, {Xiao Xuan} and Zhou, {Zhen Yu} and Chen, {Xiao Hang} and Pei, {Yuan Yuan} and Liang Hu and Su, {Jin Jiang} and Cui, {Shi Dong} and Fei Wang and Xie, {Yue Yang} and Ding, {Si Yuan} and Luo, {Meng Fan} and Chou, {Chih Hung} and Chang, {Nai Wen} and Chen, {Kai Wen} and Cheng, {Yu Hsiang} and Wan, {Xin Hong} and Hsu, {Wen Lian} and Lee, {Tzong Yi} and Wei, {Feng Xiang} and Huang, {Hsien Da}",

note = "Funding Information: Warshel Institute for Computational Biology funding from Shenzhen City and Longgang District; Ganghong Young Scholar Development Fund of Shenzhen Ganghong Group Co., Ltd. {\textquoteleft}Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B){\textquoteright} from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (MOE) in Taiwan. Conflict of interest statement. None declared. Publisher Copyright: {\textcopyright} 2019 The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2020",

month = jan,

day = "1",

doi = "10.1093/nar/gkz896",

language = "English",

volume = "48",

pages = "D148--D154",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

}

Huang, HY, Lin, YCD, Li, J, Huang, KY, Shrestha, S, Hong, HC, Tang, Y, Chen, YG, Jin, CN, Yu, Y , Xu, JT , Li, YM, Cai, XX, Zhou, ZY, Chen, XH, Pei, YY, Hu, L, Su, JJ, Cui, SD, Wang, F, Xie, YY, Ding, SY, Luo, MF, Chou, CH, Chang, NW, Chen, KW, Cheng, YH, Wan, XH, Hsu, WL, Lee, TY, Wei, FX & Huang, HD 2020, 'MiRTarBase 2020: Updates to the experimentally validated microRNA-target interaction database', Nucleic Acids Research, vol. 48, no. D1, pp. D148-D154. https://doi.org/10.1093/nar/gkz896

MiRTarBase 2020 : Updates to the experimentally validated microRNA-target interaction database. / Huang, Hsi Yuan; Lin, Yang Chi Dung; Li, Jing; Huang, Kai Yao; Shrestha, Sirjana; Hong, Hsiao Chin; Tang, Yun; Chen, Yi Gang; Jin, Chen Nan; Yu, Yuan ; Xu, Jia Tong ; Li, Yue Ming; Cai, Xiao Xuan; Zhou, Zhen Yu; Chen, Xiao Hang; Pei, Yuan Yuan; Hu, Liang; Su, Jin Jiang; Cui, Shi Dong; Wang, Fei; Xie, Yue Yang; Ding, Si Yuan; Luo, Meng Fan; Chou, Chih Hung; Chang, Nai Wen; Chen, Kai Wen; Cheng, Yu Hsiang; Wan, Xin Hong; Hsu, Wen Lian; Lee, Tzong Yi; Wei, Feng Xiang; Huang, Hsien Da.

In: Nucleic Acids Research, Vol. 48, No. D1, 01.01.2020, p. D148-D154.

Research output: Journal Publication › Article › peer-review

TY - JOUR

T1 - MiRTarBase 2020

T2 - Updates to the experimentally validated microRNA-target interaction database

AU - Huang, Hsi Yuan

AU - Lin, Yang Chi Dung

AU - Li, Jing

AU - Huang, Kai Yao

AU - Shrestha, Sirjana

AU - Hong, Hsiao Chin

AU - Tang, Yun

AU - Chen, Yi Gang

AU - Jin, Chen Nan

AU - Yu, Yuan

AU - Xu, Jia Tong

AU - Li, Yue Ming

AU - Cai, Xiao Xuan

AU - Zhou, Zhen Yu

AU - Chen, Xiao Hang

AU - Pei, Yuan Yuan

AU - Hu, Liang

AU - Su, Jin Jiang

AU - Cui, Shi Dong

AU - Wang, Fei

AU - Xie, Yue Yang

AU - Ding, Si Yuan

AU - Luo, Meng Fan

AU - Chou, Chih Hung

AU - Chang, Nai Wen

AU - Chen, Kai Wen

AU - Cheng, Yu Hsiang

AU - Wan, Xin Hong

AU - Hsu, Wen Lian

AU - Lee, Tzong Yi

AU - Wei, Feng Xiang

AU - Huang, Hsien Da

N1 - Funding Information: Warshel Institute for Computational Biology funding from Shenzhen City and Longgang District; Ganghong Young Scholar Development Fund of Shenzhen Ganghong Group Co., Ltd. ‘Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B)’ from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (MOE) in Taiwan. Conflict of interest statement. None declared. Publisher Copyright: © 2019 The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2020/1/1

Y1 - 2020/1/1

N2 - MicroRNAs (miRNAs) are small non-coding RNAs (typically consisting of 18-25 nucleotides) that negatively control expression of target genes at the post-transcriptional level. Owing to the biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA-target interactions (MTIs). To date, the database has accumulated >13,404 validated MTIs from 11,021 articles from manual curations. In this update, a text-mining system was incorporated to enhance the recognition of MTI-related articles by adopting a scoring system. In addition, a variety of biological databases were integrated to provide information on the regulatory network of miRNAs and its expression in blood. Not only targets of miRNAs but also regulators of miRNAs are provided to users for investigating the up-and downstream regulations of miRNAs. Moreover, the number of MTIs with high-throughput experimental evidence increased remarkably (validated by CLIP-seq technology). In conclusion, these improvements promote the miRTarBase as one of the most comprehensively annotated and experimentally validated miRNA-target interaction databases. The updated version of miRTarBase is now available at http://miRTarBase.cuhk.edu.cn/.

AB - MicroRNAs (miRNAs) are small non-coding RNAs (typically consisting of 18-25 nucleotides) that negatively control expression of target genes at the post-transcriptional level. Owing to the biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA-target interactions (MTIs). To date, the database has accumulated >13,404 validated MTIs from 11,021 articles from manual curations. In this update, a text-mining system was incorporated to enhance the recognition of MTI-related articles by adopting a scoring system. In addition, a variety of biological databases were integrated to provide information on the regulatory network of miRNAs and its expression in blood. Not only targets of miRNAs but also regulators of miRNAs are provided to users for investigating the up-and downstream regulations of miRNAs. Moreover, the number of MTIs with high-throughput experimental evidence increased remarkably (validated by CLIP-seq technology). In conclusion, these improvements promote the miRTarBase as one of the most comprehensively annotated and experimentally validated miRNA-target interaction databases. The updated version of miRTarBase is now available at http://miRTarBase.cuhk.edu.cn/.

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U2 - 10.1093/nar/gkz896

DO - 10.1093/nar/gkz896

M3 - Article

C2 - 31647101

AN - SCOPUS:85077235594

VL - 48

SP - D148-D154

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - D1

ER -

MiRTarBase 2020: Updates to the experimentally validated microRNA-target interaction database

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