title: miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database.
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.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Chih-Hung
authors.initials: CH
authors.lastname: Chou
authors.affiliation: Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 106, Taiwan.
authors.forename: Nai-Wen
authors.initials: NW
authors.lastname: Chang
authors.affiliation: Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Sirjana
authors.initials: S
authors.lastname: Shrestha
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Sheng-Da
authors.initials: SD
authors.lastname: Hsu
authors.affiliation: Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Yu-Ling
authors.initials: YL
authors.lastname: Lin
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan Clinical Research Center, Chung Shan Medical University Hospital, Taichung, 402, Taiwan.
authors.forename: Wei-Hsiang
authors.initials: WH
authors.lastname: Lee
authors.affiliation: 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.
authors.forename: Chi-Dung
authors.initials: CD
authors.lastname: Yang
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Hsiao-Chin
authors.initials: HC
authors.lastname: Hong
authors.affiliation: Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan.
authors.forename: Ting-Yen
authors.initials: TY
authors.lastname: Wei
authors.affiliation: Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Siang-Jyun
authors.initials: SJ
authors.lastname: Tu
authors.affiliation: Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Tzi-Ren
authors.initials: TR
authors.lastname: Tsai
authors.affiliation: Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Shu-Yi
authors.initials: SY
authors.lastname: Ho
authors.affiliation: Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Ting-Yan
authors.initials: TY
authors.lastname: Jian
authors.affiliation: Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Hsin-Yi
authors.initials: HY
authors.lastname: Wu
authors.affiliation: Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Pin-Rong
authors.initials: PR
authors.lastname: Chen
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Nai-Chieh
authors.initials: NC
authors.lastname: Lin
authors.affiliation: Degree Program of Applied Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Hsin-Tzu
authors.initials: HT
authors.lastname: Huang
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Tzu-Ling
authors.initials: TL
authors.lastname: Yang
authors.affiliation: Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
authors.forename: Chung-Yuan
authors.initials: CY
authors.lastname: Pai
authors.affiliation: 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.
authors.forename: Chun-San
authors.initials: CS
authors.lastname: Tai
authors.affiliation: 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.
authors.forename: Wen-Liang
authors.initials: WL
authors.lastname: Chen
authors.affiliation: 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.
authors.forename: Chia-Yen
authors.initials: CY
authors.lastname: Huang
authors.affiliation: Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.
authors.forename: Chun-Chi
authors.initials: CC
authors.lastname: Liu
authors.affiliation: 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.
authors.forename: Shun-Long
authors.initials: SL
authors.lastname: Weng
authors.affiliation: 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.
authors.forename: Kuang-Wen
authors.initials: KW
authors.lastname: Liao
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan hsu@iis.sinica.edu.tw.
authors.forename: Wen-Lian
authors.initials: WL
authors.lastname: Hsu
authors.affiliation: 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.
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
mesh_terms: D030561:Databases, Nucleic Acid; D004194:Disease / Q000235:genetics; D020869:Gene Expression Profiling; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger