miRTarBase 2016: Updates to the experimentally validated miRNA-target interactions database

Chih Hung Chou, Nai Wen Chang, Sirjana Shrestha, Sheng Da Hsu, Yu Ling Lin, Wei Hsiang Lee, Chi Dung Yang, Hsiao Chin Hong, Ting Yen Wei, Siang Jyun Tu, Tzi Ren Tsai, Shu Yi Ho, Ting Yan Jian, Hsin Yi Wu, Pin Rong Chen, Nai Chieh Lin, Hsin Tzu Huang, Tzu Ling Yang, Chung Yuan Pai, Chun San TaiWen-Liang Chen, Chia Yen Huang, Chun Chi Liu, Shun Long Weng, Kuang-Wen Liao, Wen Lian Hsu, Hsien Da Huang*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

710 Scopus citations

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTar-Base (http://miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target interactions (MTIs). The latest update of the miRTarBase expanded it to identify systematically Argonaute-miRNA-RNA interactions from 138 crosslinking and immunoprecipitation sequencing (CLIP-seq) data sets that were generated by 21 independent studies. The database contains 4966 articles, 7439 strongly validated MTIs (using reporter assays or western blots) and 348 007 MTIs from CLIP-seq. The number of MTIs in the miRTarBase has increased around 7-fold since the 2014 miRTar-Base update. The miRNA and gene expression profiles from The Cancer Genome Atlas (TCGA) are integrated to provide an effective overview of this exponential growth in the miRNA experimental data. These improvements make the miRTarBase one of the more comprehensively annotated, experimentally validated miRNA-target interactions databases and motivate additional miRNA research efforts.

Original languageEnglish
Pages (from-to)D239-D247
JournalNucleic acids research
Volume44
Issue numberD1
DOIs
StatePublished - 1 Jan 2016

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