miRBase: integrating microRNA annotation and deep-sequencing data

TLDR

miRBase is the primary online repository for all microRNA sequences and annotations, and deep‑sequencing technologies have sharply increased the discovery of novel microRNAs. The authors mapped short‑RNA deep‑sequencing reads to miRBase entries and built web interfaces that let users view, filter, and search read data by experiment, count, tissue, and developmental stage. The current miRBase 16 release includes over 15,000 microRNA loci and 17,000 mature sequences, and the mapped read data provide proxy expression levels, support for annotations and isoforms, and opportunities to revise earlier annotations. miRBase is available online at http://www.mirbase.org/.

Abstract

miRBase is the primary online repository for all microRNA sequences and annotation. The current release (miRBase 16) contains over 15 000 microRNA gene loci in over 140 species, and over 17 000 distinct mature microRNA sequences. Deep-sequencing technologies have delivered a sharp rise in the rate of novel microRNA discovery. We have mapped reads from short RNA deep-sequencing experiments to microRNAs in miRBase and developed web interfaces to view these mappings. The user can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression. These data can be used as a proxy for relative expression levels of microRNA sequences, provide detailed evidence for microRNA annotations and alternative isoforms of mature microRNAs, and allow us to revisit previous annotations. miRBase is available online at: http://www.mirbase.org/ .