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Nucleic Acids Res. 2016 Jan 4;44(D1):D239-47. doi: 10.1093/nar/gkv1258. Epub 2015 Nov 20.

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

Author information

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.

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.

PMID:
26590260
PMCID:
PMC4702890
DOI:
10.1093/nar/gkv1258
[Indexed for MEDLINE]
Free PMC Article

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