Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jan 6;51(D1):D179-D185.
doi: 10.1093/nar/gkac884.

isomiRdb: microRNA expression at isoform resolution

Ernesto Aparicio-Puerta  1 , Pascal Hirsch  1 , Georges P Schmartz  1 , Tobias Fehlmann  1   2 , Verena Keller  1   3 , Annika Engel  1 , Fabian Kern  1   4 , Michael Hackenberg  5 , Andreas Keller  1   4
Affiliations

isomiRdb: microRNA expression at isoform resolution

Ernesto Aparicio-Puerta et al. Nucleic Acids Res. .

Abstract

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 using miRMaster 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.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Development process and functionalities of isomiRdb. In short, 42 499 miRNA-seq samples from TCGA, SRA and provided by miRMaster users were uniformly processed to offer tissue and cell type expression levels of miRNAs at isomiR resolution. Tissue/cell specificity index and several types of visualizations are available.
Figure 2.
Figure 2.
Different visualizations of miR-21–5p expression. (A) Mean expression of miR-21-5p per tissue. (B) Mean expression of miR-21-5p per cell type. (C) Heatmap of miR-21-5p isomiRs. A NTA-U isoform described in the use case is highlighted in red.
See this image and copyright information in PMC

References

    1. Gebert L.F.R., MacRae I.J.. Regulation of microRNA function in animals. Nat. Rev. Mol. Cell Biol. 2018; 20:21–37. - PMC - PubMed
    1. Valencia-Sanchez M.A., Liu J., Hannon G.J., Parker R.. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 2006; 20:515–524. - PubMed
    1. Friedman R.C., Farh K.K.H., Burge C.B., Bartel D.P.. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009; 19:92–105. - PMC - PubMed
    1. Keller A., Leidinger P., Vogel B., Backes C., ElSharawy A., Galata V., Mueller S.C., Marquart S., Schrauder M.G., Strick R.et al. .. miRNAs can be generally associated with human pathologies as exemplified for miR-144. BMC Med. 2014; 12:224. - PMC - PubMed
    1. Landgraf P., Rusu M., Sheridan R., Sewer A., Iovino N., Aravin A., Pfeffer S., Rice A., Kamphorst A.O., Landthaler M.et al. .. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell. 2007; 129:1401–1414. - PMC - PubMed

Publication types