miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions

Hsi‐Yuan Huang(Shenzhen Maternity and Child Healthcare Hospital), Yang-Chi-Dung Lin(Shenzhen Maternity and Child Healthcare Hospital), Shidong Cui(Chinese University of Hong Kong, Shenzhen), Yixian Huang(Chinese University of Hong Kong, Shenzhen), Yun Tang(Chinese University of Hong Kong, Shenzhen), Jiatong Xu(Chinese University of Hong Kong, Shenzhen), Jiayang Bao(University of California San Diego), Yulin Li(Chinese University of Hong Kong, Shenzhen), Jia Wen(Chinese University of Hong Kong, Shenzhen), Hua‐Li Zuo(University of Science and Technology of China), Weijuan Wang(Chinese University of Hong Kong, Shenzhen), Jing Li(Chinese University of Hong Kong, Shenzhen), Jie Ni(Chinese University of Hong Kong, Shenzhen), Yini Ruan(Chinese University of Hong Kong, Shenzhen), Liping Li(Chinese University of Hong Kong, Shenzhen), Yidan Chen(Chinese University of Hong Kong, Shenzhen), Yueyang Xie(Chinese University of Hong Kong, Shenzhen), Zihao Zhu(Chinese University of Hong Kong, Shenzhen), Xiaoxuan Cai(Chinese University of Hong Kong, Shenzhen), Xinyi Chen(Chinese University of Hong Kong, Shenzhen), Lantian Yao(Chinese University of Hong Kong, Shenzhen), Yi-Gang Chen(Chinese University of Hong Kong, Shenzhen), Yijun Luo(Chinese University of Hong Kong, Shenzhen), Shupeng Luxu(Chinese University of Hong Kong, Shenzhen), Mengqi Luo(Chinese University of Hong Kong, Shenzhen), Chih-Min Chiu(Chinese University of Hong Kong, Shenzhen), Kun Ma(Chinese University of Hong Kong, Shenzhen), Lizhe Zhu(Chinese University of Hong Kong, Shenzhen), Gui‐Juan Cheng(Chinese University of Hong Kong, Shenzhen), Chen Bai(Chinese University of Hong Kong, Shenzhen), Ying‐Chih Chiang(Chinese University of Hong Kong, Shenzhen), Liping Wang(Shenzhen Second People's Hospital), Fengxiang Wei(Jiamusi University), Tzong-Yi Lee(Chinese University of Hong Kong, Shenzhen), Hsien‐Da Huang(Shenzhen Maternity and Child Healthcare Hospital)
Nucleic Acids Research
October 25, 2021
10.1093/nar/gkab1079
Cited by 1,029Open Access
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Abstract

Abstract MicroRNAs (miRNAs) are noncoding RNAs with 18–26 nucleotides; they pair with target mRNAs to regulate gene expression and produce significant changes in various physiological and pathological processes. In recent years, the interaction between miRNAs and their target genes has become one of the mainstream directions for drug development. As a large-scale biological database that mainly provides miRNA–target interactions (MTIs) verified by biological experiments, miRTarBase has undergone five revisions and enhancements. The database has accumulated >2 200 449 verified MTIs from 13 389 manually curated articles and CLIP-seq data. An optimized scoring system is adopted to enhance this update’s critical recognition of MTI-related articles and corresponding disease information. In addition, single-nucleotide polymorphisms and disease-related variants related to the binding efficiency of miRNA and target were characterized in miRNAs and gene 3′ untranslated regions. miRNA expression profiles across extracellular vesicles, blood and different tissues, including exosomal miRNAs and tissue-specific miRNAs, were integrated to explore miRNA functions and biomarkers. For the user interface, we have classified attributes, including RNA expression, specific interaction, protein expression and biological function, for various validation experiments related to the role of miRNA. We also used seed sequence information to evaluate the binding sites of miRNA. In summary, these enhancements render miRTarBase as one of the most research-amicable MTI databases that contain comprehensive and experimentally verified annotations. The newly updated version of miRTarBase is now available at https://miRTarBase.cuhk.edu.cn/.

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