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

Chih-Hung Chou¹, Nai-Wen Chang², Sirjana Shrestha³, Sheng-Da Hsu¹, Yu-Ling Lin⁴, Wei-Hsiang Lee⁵, Chi-Dung Yang⁶, Hsiao-Chin Hong¹, Ting-Yen Wei⁷, Siang-Jyun Tu³, Tzi-Ren Tsai³, Shu-Yi Ho³, Ting-Yan Jian⁸, Hsin-Yi Wu⁸, Pin-Rong Chen⁸, Nai-Chieh Lin¹, Hsin-Tzu Huang⁹, Tzu-Ling Yang¹, Chung-Yuan Pai⁸, Chun-San Tai¹⁰, Wen-Liang Chen¹¹, Chia-Yen Huang¹², Chun-Chi Liu¹³, Shun-Long Weng¹⁴, Kuang-Wen Liao¹⁵, Wen-Lian Hsu¹⁶, Hsien-Da Huang¹⁷

Affiliations

¹ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
² Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 106, Taiwan.
³ Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
⁴ Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 300, Taiwan.
⁵ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan Clinical Research Center, Chung Shan Medical University Hospital, Taichung, 402, Taiwan.
⁶ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 350, Taiwan.
⁷ Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan.
⁸ Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
⁹ Degree Program of Applied Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
¹⁰ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
¹¹ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
¹² Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General Hospital, Taipei, 106, Taiwan.
¹³ Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.
¹⁴ Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, 300, Taiwan Mackay Medicine, Nursing and Management College, Taipei, 112, Taiwan Department of Medicine, Mackay Medical College, New Taipei City, 252, Taiwan.
¹⁵ Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
¹⁶ Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan hsu@iis.sinica.edu.tw.
¹⁷ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 300, Taiwan Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan bryan@mail.nctu.edu.tw.

PMID: 26590260
PMCID: PMC4702890
DOI: 10.1093/nar/gkv1258

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

Chih-Hung Chou et al. Nucleic Acids Res. 2016.

. 2016 Jan 4;44(D1):D239-47.

doi: 10.1093/nar/gkv1258. Epub 2015 Nov 20.

Authors

Affiliations

¹ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
² Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 106, Taiwan.
³ Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
⁴ Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 300, Taiwan.
⁵ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan Clinical Research Center, Chung Shan Medical University Hospital, Taichung, 402, Taiwan.
⁶ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 350, Taiwan.
⁷ Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan.
⁸ Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
⁹ Degree Program of Applied Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
¹⁰ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
¹¹ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
¹² Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General Hospital, Taipei, 106, Taiwan.
¹³ Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.
¹⁴ Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, 300, Taiwan Mackay Medicine, Nursing and Management College, Taipei, 112, Taiwan Department of Medicine, Mackay Medical College, New Taipei City, 252, Taiwan.
¹⁵ Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
¹⁶ Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan hsu@iis.sinica.edu.tw.
¹⁷ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 300, Taiwan Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan bryan@mail.nctu.edu.tw.

PMID: 26590260
PMCID: PMC4702890
DOI: 10.1093/nar/gkv1258

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.

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Figures

**Figure 1.**
Snapshot of major improvements provided by miRTarBase interface. (A) New miRTarBase home page and three new major interfaces, including miRNA disease word cloud (B), miRNA-target site viewer based on CLIP-seq data (C) and miRNA and gene expression profiles obtained using TCGA data set (D).

**Figure 2.**
Natural language processing (NLP) techniques for finding MTI articles. (i) Articles collected from PubMed; (ii) preprocessing articles in the following steps; split sentences, tokenization, stemming and stopword removal; (**iii**) Named Entity Recognition (NER) based on principle-based approach (PBA), Conditional Random Field (CRF) and dictionary-based approach; (iv) following construction and evaluation of model, MTI extraction protocol was developed using PBA; (v) all curated articles were manually evaluated by biological domain experts.

See this image and copyright information in PMC

References

1. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116:281–297. - PubMed
1. Engels B.M., Hutvagner G. Principles and effects of microRNA-mediated post-transcriptional gene regulation. Oncogene. 2006;25:6163–6169. - PubMed
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1. Lynam-Lennon N., Maher S.G., Reynolds J.V. The roles of microRNA in cancer and apoptosis. Biol. Rev. Camb. Philos. Soc. 2009;84:55–71. - PubMed

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

Affiliations

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

Authors

Affiliations

Abstract

Figures

References

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MeSH terms

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LinkOut - more resources

Full Text Sources

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