title: 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.
authors.affiliation: Division of Pediatric Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei 11217, Taiwan.
authors.forename: Wei-Chung
authors.initials: WC
authors.lastname: Cheng
authors.forename: I-Fang
authors.initials: IF
authors.lastname: Chung
authors.forename: Tse-Shun
authors.initials: TS
authors.lastname: Huang
authors.forename: Shih-Ting
authors.initials: ST
authors.lastname: Chang
authors.forename: Hsing-Jen
authors.initials: HJ
authors.lastname: Sun
authors.forename: Cheng-Fong
authors.initials: CF
authors.lastname: Tsai
authors.forename: Muh-Lii
authors.initials: ML
authors.lastname: Liang
authors.forename: Tai-Tong
authors.initials: TT
authors.lastname: Wong
authors.forename: Hsei-Wei
authors.initials: HW
authors.lastname: Wang
mesh_terms: D030561:Databases, Nucleic Acid; D020407:Internet; D035683:MicroRNAs / Q000737:chemistry* / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014584:User-Computer Interface
chemical_list: D035683:MicroRNAs