YM500: A small RNA sequencing (smRNA-seq) database for microRNA research

Wei Chung Cheng, I. Fang Chung, Tse Shun Huang, Shih Ting Chang, Hsing Jen Sun, Cheng Fong Tsai, Muh Lii Liang, Tai-Tong Wong, Hsei Wei Wang

Research output: Contribution to journalArticle

38 Citations (Scopus)

Abstract

MicroRNAs (miRNAs) are small RNAs ∼22 nt in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next-generation sequencing applications, have reshaped the miRNA research landscape. In this study, we established an integrative database, the YM500 (http://ngs.ym. edu.tw/ym500/), containing analysis pipelines and analysis results for 609 human and mice smRNA-seq results, including public data from the Gene Expression Omnibus (GEO) and some private sources. YM500 collects analysis results for miRNA quantification, for isomiR identification (incl. RNA editing), for arm switching discovery, and, more importantly, for novel miRNA predictions. Wetlab validation on >100 miRNAs confirmed high correlation between miRNA profiling and RT-qPCR results (R = 0.84). This database allows researchers to search these four different types of analysis results via our interactive web interface. YM500 allows researchers to define the criteria of isomiRs, and also integrates the information of dbSNP to help researchers distinguish isomiRs from SNPs. A user-friendly interface is provided to integrate miRNA-related information and existing evidence from hundreds of sequencing datasets. The identified novel miRNAs and isomiRs hold the potential for both basic research and biotech applications.

Original languageEnglish
JournalNucleic Acids Research
Volume41
Issue numberD1
DOIs
Publication statusPublished - Jan 1 2013
Externally publishedYes

Fingerprint

RNA Sequence Analysis
Nucleic Acid Databases
MicroRNAs
Research
Research Personnel
Databases
Physiological Phenomena
RNA Editing
High-Throughput Nucleotide Sequencing
Pathologic Processes
Single Nucleotide Polymorphism
RNA
Gene Expression

ASJC Scopus subject areas

  • Genetics

Cite this

Cheng, W. C., Chung, I. F., Huang, T. S., Chang, S. T., Sun, H. J., Tsai, C. F., ... Wang, H. W. (2013). YM500: A small RNA sequencing (smRNA-seq) database for microRNA research. Nucleic Acids Research, 41(D1). https://doi.org/10.1093/nar/gks1238

YM500 : A small RNA sequencing (smRNA-seq) database for microRNA research. / Cheng, Wei Chung; Chung, I. Fang; Huang, Tse Shun; Chang, Shih Ting; Sun, Hsing Jen; Tsai, Cheng Fong; Liang, Muh Lii; Wong, Tai-Tong; Wang, Hsei Wei.

In: Nucleic Acids Research, Vol. 41, No. D1, 01.01.2013.

Research output: Contribution to journalArticle

Cheng, WC, Chung, IF, Huang, TS, Chang, ST, Sun, HJ, Tsai, CF, Liang, ML, Wong, T-T & Wang, HW 2013, 'YM500: A small RNA sequencing (smRNA-seq) database for microRNA research', Nucleic Acids Research, vol. 41, no. D1. https://doi.org/10.1093/nar/gks1238
Cheng WC, Chung IF, Huang TS, Chang ST, Sun HJ, Tsai CF et al. YM500: A small RNA sequencing (smRNA-seq) database for microRNA research. Nucleic Acids Research. 2013 Jan 1;41(D1). https://doi.org/10.1093/nar/gks1238
Cheng, Wei Chung ; Chung, I. Fang ; Huang, Tse Shun ; Chang, Shih Ting ; Sun, Hsing Jen ; Tsai, Cheng Fong ; Liang, Muh Lii ; Wong, Tai-Tong ; Wang, Hsei Wei. / YM500 : A small RNA sequencing (smRNA-seq) database for microRNA research. In: Nucleic Acids Research. 2013 ; Vol. 41, No. D1.
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