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miRTarBase 2020:实验验证的 microRNA-靶标相互作用数据库更新。

miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database.

机构信息

School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China.

Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China.

出版信息

Nucleic Acids Res. 2020 Jan 8;48(D1):D148-D154. doi: 10.1093/nar/gkz896.


DOI:10.1093/nar/gkz896
PMID:31647101
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7145596/
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/.

摘要

微小 RNA(miRNAs)是小的非编码 RNA(通常由 18-25 个核苷酸组成),在转录后水平上负调控靶基因的表达。由于 miRNAs 的生物学意义,miRTarBase 被开发出来,以提供实验验证的 miRNA-靶相互作用(MTIs)的综合信息。迄今为止,该数据库已从手动注释的 11021 篇文章中积累了超过 13404 个验证的 MTIs。在本次更新中,采用评分系统纳入了文本挖掘系统,以增强对 MTI 相关文章的识别。此外,还整合了各种生物数据库,提供 miRNA 调控网络及其在血液中的表达信息。不仅为用户提供了 miRNA 的靶标,还提供了 miRNA 的调控因子,以研究 miRNA 的上下游调控。此外,具有高通量实验证据的 MTIs 的数量显著增加(通过 CLIP-seq 技术验证)。总之,这些改进促进了 miRTarBase 成为最全面注释和实验验证的 miRNA-靶相互作用数据库之一。miRTarBase 的更新版本可在 http://miRTarBase.cuhk.edu.cn/ 获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/de21/7145596/f8ea61e406e3/gkz896fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/de21/7145596/cbe43f0087b7/gkz896fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/de21/7145596/f8ea61e406e3/gkz896fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/de21/7145596/cbe43f0087b7/gkz896fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/de21/7145596/f8ea61e406e3/gkz896fig2.jpg

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[2]
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本文引用的文献

[1]
Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition: Bioinformatics Resources.

Methods Mol Biol. 2019

[2]
Exosomal microRNA profiles from serum and cerebrospinal fluid in neurosyphilis.

Sex Transm Infect. 2019-3-29

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CMEP: a database for circulating microRNA expression profiling.

Bioinformatics. 2019-9-1

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Nucleic Acids Res. 2019-1-8

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Nucleic Acids Res. 2019-1-8

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miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions.

Nucleic Acids Res. 2018-1-4

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Nucleic Acids Res. 2018-1-4

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Abnormal expression of mRNA, microRNA alteration and aberrant DNA methylation patterns in rectal adenocarcinoma.

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