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

Chih-Hung Chou; Sirjana Shrestha; Chi-Dung Yang; Nai-Wen Chang; Yu-Ling Lin; Kuang-Wen Liao; Wei-Chi Huang; Ting-Hsuan Sun; Siang-Jyun Tu; Wei-Hsiang Lee; Men-Yee Chiew; Chun-San Tai; Ting-Yen Wei; Tzi-Ren Tsai; Hsin-Tzu Huang; Chung-Yu Wang; Hsin-Yi Wu; Shu-Yi Ho; Pin-Rong Chen; Cheng-Hsun Chuang; Pei-Jung Hsieh; Yi-Shin Wu; Wen-Liang Chen; Meng-Ju Li; Yu-Chun Wu; Xin-Yi Huang; Fung Ling Ng; Waradee Buddhakosai; Pei-Chun Huang; Kuan-Chun Lan; Chia-Yen Huang; Shun-Long Weng; Yeong-Nan Cheng; Chao Liang; Wen-Lian Hsu; Hsien-Da Huang

doi:10.1093/nar/gkx1067

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

Nucleic Acids Res. 2018 Jan 4;46(D1):D296-D302. doi: 10.1093/nar/gkx1067.

Authors

Chih-Hung Chou^{1

2}, Sirjana Shrestha², Chi-Dung Yang^{2

3}, Nai-Wen Chang⁴, Yu-Ling Lin^{2

5}, Kuang-Wen Liao^{2

6}, Wei-Chi Huang^{1

2}, Ting-Hsuan Sun², Siang-Jyun Tu¹, Wei-Hsiang Lee^{2

7}, Men-Yee Chiew², Chun-San Tai², Ting-Yen Wei⁸, Tzi-Ren Tsai², Hsin-Tzu Huang², Chung-Yu Wang⁶, Hsin-Yi Wu⁶, Shu-Yi Ho², Pin-Rong Chen⁶, Cheng-Hsun Chuang⁶, Pei-Jung Hsieh², Yi-Shin Wu², Wen-Liang Chen², Meng-Ju Li^{2

9}, Yu-Chun Wu², Xin-Yi Huang², Fung Ling Ng², Waradee Buddhakosai², Pei-Chun Huang¹⁰, Kuan-Chun Lan⁶, Chia-Yen Huang^{2

11}, Shun-Long Weng^{12

13

14}, Yeong-Nan Cheng¹, Chao Liang¹, Wen-Lian Hsu¹⁵, Hsien-Da Huang^{1

2

16

17}

Affiliations

¹ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
² Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
³ Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 350, Taiwan.
⁴ Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 106, Taiwan.
⁵ Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 300, Taiwan.
⁶ Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
⁷ Clinical Research Center, Chung Shan Medical University Hospital, Taichung, 402, Taiwan.
⁸ Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan.
⁹ Department of Pediatrics, National Taiwan University Hospital Hsinchu Branch, Hsinchu, 300, Taiwan.
¹⁰ Delivery Room, Department of Nursing, National Taiwan University Hospital Hsinchu Branch, Hsinchu, 300, Taiwan.
¹¹ Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General Hospital, Taipei, 106, Taiwan.
¹² Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, 300, Taiwan.
¹³ Mackay Medicine, Nursing and Management College, Taipei, 112, Taiwan.
¹⁴ Department of Medicine, Mackay Medical College, New Taipei City, 252, Taiwan.
¹⁵ Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan.
¹⁶ Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong Province, 518172, China.
¹⁷ School of Science and Engineering, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong Province, 518172, China.

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 22 nucleotides that are involved in negative regulation of mRNA at the post-transcriptional level. Previously, we developed miRTarBase which provides information about experimentally validated miRNA-target interactions (MTIs). Here, we describe an updated database containing 422 517 curated MTIs from 4076 miRNAs and 23 054 target genes collected from over 8500 articles. The number of MTIs curated by strong evidence has increased ∼1.4-fold since the last update in 2016. In this updated version, target sites validated by reporter assay that are available in the literature can be downloaded. The target site sequence can extract new features for analysis via a machine learning approach which can help to evaluate the performance of miRNA-target prediction tools. Furthermore, different ways of browsing enhance user browsing specific MTIs. With these improvements, miRTarBase serves as more comprehensively annotated, experimentally validated miRNA-target interactions databases in the field of miRNA related research. miRTarBase is available at http://miRTarBase.mbc.nctu.edu.tw/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Data Mining
Databases, Genetic*
Humans
MicroRNAs / metabolism*
RNA, Messenger / chemistry
RNA, Messenger / metabolism*
User-Computer Interface

Substances

MicroRNAs
RNA, Messenger