miRBase: from microRNA sequences to function

Abstract

miRBase catalogs, names and distributes microRNA gene sequences. The latest release of miRBase (v22) contains microRNA sequences from 271 organisms: 38 589 hairpin precursors and 48 860 mature microRNAs. We describe improvements to the database and website to provide more information about the quality of microRNA gene annotations, and the cellular functions of their products. We have collected 1493 small RNA deep sequencing datasets and mapped a total of 5.5 billion reads to microRNA sequences. The read mapping patterns provide strong support for the validity of between 20% and 65% of microRNA annotations in different well-studied animal genomes, and evidence for the removal of >200 sequences from the database. To improve the availability of microRNA functional information, we are disseminating Gene Ontology terms annotated against miRBase sequences. We have also used a text-mining approach to search for microRNA gene names in the full-text of open access articles. Over 500 000 sentences from 18 542 papers contain microRNA names. We score these sentences for functional information and link them with 12 519 microRNA entries. The sentences themselves, and word clouds built from them, provide effective summaries of the functional information about specific microRNAs. miRBase is publicly and freely available at http://mirbase.org/.

Figure 1.

The proportion of microRNA sequences annotated as high confidence in release 22 (black) and release 21 (grey). All species with 30 or more small RNA deep sequencing datasets in miRBase 22 are shown. Species abbreviations: dre: Danio rerio; rno: Rattus norvegicus; dme: Drosophila melanogaster; cel: Caenorhabditis elegans; mmu: Mus musculus, zma: Zea mays; hsa: Homo sapiens; bta: Bos taurus; tae: Triticum aestivum.

Figure 2.

MicroRNA functional information mined from open access papers. (A) The top 20 species according to the number of open access papers associated with their microRNAs. (B) The proportion of microRNAs from selected model organisms that have papers and sentences associated. (C) Word cloud for Drosophila melanogaster bantam microRNA. (D) Word cloud for hsa-mir-133a-2. Species abbreviations: hsa: Homo sapiens, mmu: Mus musculus, rno: Rattus norvegicus; dme: Drosophila melanogaster; ath: Arabidopsis thaliana; osa: Oryza sativa; dre: Danio rerio; bta: Bos taurus; gga: Gallus gallus; cel: Caenorhabditis elegans; ssc: Sus scrofa; zma: Zea mays; sly: Solanum lycopersicum; tae: Triticum aestivum; gma: Glycine max; oar: Ovis aries; ghr: Gossypium hirsutum; hvu: Hordeum vulgare; ocu: Oryctolagus cuniculus; chi: Capra hircus.