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J. Clin. Med. 2015, 4(9), 1798-1814; doi:10.3390/jcm4091798

Bioinformatic Interrogation of 5p-arm and 3p-arm Specific miRNA Expression Using TCGA Datasets

1
Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
2
Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan
3
Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 100, Taiwan
4
Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei 112,Taiwan
*
Author to whom correspondence should be addressed.
Academic Editors: Takahiro Ochiya and Ryou-u Takahashi
Received: 23 June 2015 / Revised: 25 August 2015 / Accepted: 9 September 2015 / Published: 15 September 2015
(This article belongs to the Special Issue MicroRNAs: Novel Biomarkers and Therapeutic Targets for Human Cancers)
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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. View Full-Text
Keywords: microRNA; 5p-arm; 3p-arm; bioinformatics; TCGA; biomarker microRNA; 5p-arm; 3p-arm; bioinformatics; TCGA; biomarker
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MDPI and ACS Style

Kuo, W.-T.; Su, M.-W.; Lee, Y.L.; Chen, C.-H.; Wu, C.-W.; Fang, W.-L.; Huang, K.-H.; Lin, W.-C. Bioinformatic Interrogation of 5p-arm and 3p-arm Specific miRNA Expression Using TCGA Datasets. J. Clin. Med. 2015, 4, 1798-1814.

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