Institute of Information Science, Academia Sinica

It has become clear that high-throughput genomics tools are powerful in filtrating out novel biomarkers and therapeutic targets from clinical samples with high level of heterogeneity. MicroRNAs (miRNAs) are small RNAs approximately 22 nucleotides in length that are involved in the regulation of a variety of physiological and pathological processes. Circulating miRNAs in plasma hold the potential to be novel biomarkers.  Recent 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, 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 (Nucleic Acids Research, 2012, in press). 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. We recently found that miR-31 is a novel lymphangiogenic microRNA (Blood, Sep 2011) that is involved in the activities of circulating endothelial progenitor cells (EPCs; BMC Genomics, Sep 2012). In this talk I shall introduce more about how to study miRNAs by smRNA-seq.