isomiRdb: microRNA expression at isoform resolution
Metadatos
Afficher la notice complèteEditorial
Oxford University Press
Date
2022-10-16Referencia bibliográfica
Ernesto Aparicio-Puerta... [et al.]. isomiRdb: microRNA expression at isoform resolution, Nucleic Acids Research, 2022;, gkac884, [https://doi.org/10.1093/nar/gkac884]
Patrocinador
Saarland UniversityRésumé
A significant fraction of mature miRNA transcripts
carries sequence and/or length variations, termed
isomiRs. IsomiRs are differentially abundant in cell
types, tissues, body fluids or patients’ samples.
Not surprisingly, multiple studies describe a physiological
and pathophysiological role. Despite their
importance, systematically collected and annotated
isomiR information available in databases remains
limited. We thus developed isomiRdb, a comprehensive
resource that compiles miRNA expression data
at isomiR resolution from various sources. We processed
42 499 human miRNA-seq datasets (5.9×1011
sequencing reads) and consistently analyzed them
usingmiRMaster and sRNAbench. Our database provides
online access to the 90 483 most abundant
isomiRs (>1 RPM in at least 1% of the samples)
from 52 tissues and 188 cell types. Additionally, the
full set of over 3 million detected isomiRs is available
for download. Our resource can be queried
at the sample, miRNA or isomiR level so users
can quickly answer common questions about the
presence/absence of a particular miRNA/isomiR in
tissues of interest. Further, the database facilitates
to identify whether a potentially interesting new isoform
has been detected before and its frequency. In
addition to expression tables, isomiRdb can generate
multiple interactive visualisations including violin
plots and heatmaps. isomiRdb is free to use and
publicly available at: https://www.ccb.uni-saarland.
de/isomirdb.