title: Bioinformatic Interrogation of 5p-arm and 3p-arm Specific miRNA Expression Using TCGA Datasets.
abstract: MicroRNAs (miRNAs) play important roles in cellular functions and developmental processes. They are also implicated in oncogenesis mechanisms and could serve as potential cancer biomarkers. Using high-throughput miRNA sequencing information, expression of both the 5p-arm and 3p-arm mature miRNAs were demonstrated and generated from the single miRNA hairpin precursor. However, current miRNA annotations lack comprehensive 5p-arm/3p-arm feature annotations. Among known human mature miRNAs, only half of them are annotated with arm features. This generated ambiguous results in many miRNA-Sequencing (miRNA-Seq) studies. In this report, we have interrogated the TCGA (the Cancer Genome Atlas) miRNA expression datasets with an improved, fully annotated human 5p-arm and 3p-arm miRNA reference list. By utilizing this comprehensive miRNA arm-feature annotations, enhanced determinations and clear annotations were achieved for the miRNA isoforms (isomiRs) recognized from the sequencing reads. In the gastric cancer (STAD) dataset, as an example, 32 5p-arm/3p-arm OPEN ACCESS J. Clin. Med. 2015, 4 1799 specific miRNAs were found to be down-regulated and 24 5p-arm/3p-arm specific miRNAs were found to be up-regulated. We have further extended miRNA biomarker discoveries to additional TCGA miRNA-Seq datasets and provided extensive expression information on 5p-arm/3p-arm miRNAs across multiple cancer types. Our results identified several miRNAs that could be potential common biomarkers for human cancers.
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan. raxkuo@hotmail.com.|Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan. raxkuo@hotmail.com.
authors.forename: Wei-Ting
authors.initials: WT
authors.lastname: Kuo
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan. a8802137@gmail.com.|Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 100, Taiwan. a8802137@gmail.com.
authors.forename: Ming-Wei
authors.initials: MW
authors.lastname: Su
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan. leolee@ntu.edu.tw.|Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 100, Taiwan. leolee@ntu.edu.tw.
authors.forename: Yungling Leo
authors.initials: YL
authors.lastname: Lee
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan. chchen@ibms.sinica.edu.tw.
authors.forename: Chien-Hsiun
authors.initials: CH
authors.lastname: Chen
authors.affiliation: Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei 112,Taiwan. chewwunwu@gmail.com.
authors.forename: Chew-Wun
authors.initials: CW
authors.lastname: Wu
authors.affiliation: Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei 112,Taiwan. wlfang@vghtpe.gov.tw.
authors.forename: Wen-Liang
authors.initials: WL
authors.lastname: Fang
authors.affiliation: Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei 112,Taiwan. khhuang@vghtpe.gov.tw.
authors.forename: Kuo-Hung
authors.initials: KH
authors.lastname: Huang
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan. wenlin@ibms.sinica.edu.tw.|Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan. wenlin@ibms.sinica.edu.tw.
authors.forename: Wen-Chang
authors.initials: WC
authors.lastname: Lin
keywords: 3p-arm; 5p-arm; TCGA; bioinformatics; biomarker; microRNA