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

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.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Cheng WC,Chung IF,Huang TS,Chang ST,Sun HJ,Tsai CF,Liang ML,Wong TT,Wang HW

doi

10.1093/nar/gks1238

subject

Has Abstract

pub_date

2013-01-01 00:00:00

pages

D285-94

issue

Database issue

eissn

0305-1048

issn

1362-4962

pii

gks1238

journal_volume

41

pub_type

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