Next Article in Journal
Interrelation between Neuroendocrine Disturbances and Medical Complications Encountered during Rehabilitation after TBI
Next Article in Special Issue
MicroRNA Library-Based Functional Screening Identified Androgen-Sensitive miR-216a as a Player in Bicalutamide Resistance in Prostate Cancer
Previous Article in Journal
Hypothalamic Obesity in Craniopharyngioma Patients: Disturbed Energy Homeostasis Related to Extent of Hypothalamic Damage and Its Implication for Obesity Intervention
Previous Article in Special Issue
MicroRNAs and Osteolytic Bone Metastasis: The Roles of MicroRNAs in Tumor-Induced Osteoclast Differentiation

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

Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan
Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 100, Taiwan
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
J. Clin. Med. 2015, 4(9), 1798-1814;
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)
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
Show Figures

Figure 1

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.

AMA Style

Kuo W-T, Su M-W, Lee YL, 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. Journal of Clinical Medicine. 2015; 4(9):1798-1814.

Chicago/Turabian Style

Kuo, Wei-Ting, Ming-Wei Su, Yungling L. Lee, Chien-Hsiun Chen, Chew-Wun Wu, Wen-Liang Fang, Kuo-Hung Huang, and Wen-chang Lin. 2015. "Bioinformatic Interrogation of 5p-arm and 3p-arm Specific miRNA Expression Using TCGA Datasets" Journal of Clinical Medicine 4, no. 9: 1798-1814.

Find Other Styles

Article Access Map by Country/Region

Only visits after 24 November 2015 are recorded.
Back to TopTop