- miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. [PMID: 26590260]
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 Tai, Wen-Liang Chen, Chia-Yen Huang, Chun-Chi Liu, Shun-Long Weng, Kuang-Wen Liao, Wen-Lian Hsu, Hsien-Da Huang
Nucleic acids research 2016:44(D1)
164 Citations (Google Scholar as of 2017-05-17)
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 miRTarBase (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 miRTarBase 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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
- miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. [PMID: 24304892]
Sheng-Da Hsu, Yu-Ting Tseng, Sirjana Shrestha, Yu-Ling Lin, Anas Khaleel, Chih-Hung Chou, Chao-Fang Chu, Hsi-Yuan Huang, Ching-Min Lin, Shu-Yi Ho, Ting-Yan Jian, Feng-Mao Lin, Tzu-Hao Chang, Shun-Long Weng, Kuang-Wen Liao, I-En Liao, Chun-Chi Liu, Hsien-Da Huang
Nucleic acids research 2014:42(Database issue)
264 Citations (Google Scholar as of 2016-05-03)
Abstract: MicroRNAs (miRNAs) are small non-coding RNA molecules capable of negatively regulating gene expression to control many cellular mechanisms. The miRTarBase database (http://mirtarbase.mbc.nctu.edu.tw/) provides the most current and comprehensive information of experimentally validated miRNA-target interactions. The database was launched in 2010 with data sources for >100 published studies in the identification of miRNA targets, molecular networks of miRNA targets and systems biology, and the current release (2013, version 4) includes significant expansions and enhancements over the initial release (2010, version 1). This article reports the current status of and recent improvements to the database, including (i) a 14-fold increase to miRNA-target interaction entries, (ii) a miRNA-target network, (iii) expression profile of miRNA and its target gene, (iv) miRNA target-associated diseases and (v) additional utilities including an upgrade reminder and an error reporting/user feedback system.
- miRTarBase: a database curates experimentally validated microRNA-target interactions. [PMID: 21071411]
Sheng-Da Hsu, Feng-Mao Lin, Wei-Yun Wu, Chao Liang, Wei-Chih Huang, Wen-Ling Chan, Wen-Ting Tsai, Goun-Zhou Chen, Chia-Jung Lee, Chih-Min Chiu, Chia-Hung Chien, Ming-Chia Wu, Chi-Ying Huang, Ann-Ping Tsou, Hsien-Da Huang
Nucleic acids research 2011:39(Database issue)
471 Citations (Google Scholar as of 2016-05-09)
Abstract: MicroRNAs (miRNAs), i.e. small non-coding RNA molecules (∼22 nt), can bind to one or more target sites on a gene transcript to negatively regulate protein expression, subsequently controlling many cellular mechanisms. A current and curated collection of miRNA-target interactions (MTIs) with experimental support is essential to thoroughly elucidating miRNA functions under different conditions and in different species. As a database, miRTarBase has accumulated more than 3500 MTIs by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs. miRTarBase curates 3576 experimentally verified MTIs between 657 miRNAs and 2297 target genes among 17 species. miRTarBase contains the largest amount of validated MTIs by comparing with other similar, previously developed databases. The MTIs collected in the miRTarBase can also provide a large amount of positive samples to develop computational methods capable of identifying miRNA-target interactions. miRTarBase is now available on http://miRTarBase.mbc.nctu.edu.tw/, and is updated frequently by continuously surveying research articles.