Journal of Clinical Medicine | |
Bioinformatic Interrogation of 5p-arm and 3p-arm Specific miRNA Expression Using TCGA Datasets | |
Wei-Ting Kuo2  Ming-Wei Su2  Yungling Leo Lee2  Chien-Hsiun Chen2  Chew-Wun Wu1  Wen-Liang Fang1  Kuo-Hung Huang1  Wen-chang Lin2  Takahiro Ochiya3  | |
[1] Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei 112, Taiwan; E-Mails:;Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; E-Mails:Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; | |
关键词: microRNA; 5p-arm; 3p-arm; bioinformatics; TCGA; biomarker; | |
DOI : 10.3390/jcm4091798 | |
来源: mdpi | |
【 摘 要 】
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 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.
【 授权许可】
CC BY
© 2015 by the authors; licensee MDPI, Basel, Switzerland.
【 预 览 】
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