miRmine: a database of human miRNA expression profiles

Abstract

Motivation: MicroRNAs (miRNAs) are small non-coding RNAs that are involved in post-transcriptional regulation of gene expression. In this high-throughput sequencing era, a tremendous amount of RNA-seq data is accumulating, and full utilization of publicly available miRNA data is an important challenge. These data are useful to determine expression values for each miRNA, but quantification pipelines are in a primitive stage and still evolving; there are many factors that affect expression values significantly.

Results: We used 304 high-quality microRNA sequencing (miRNA-seq) datasets from NCBI-SRA and calculated expression profiles for different tissues and cell-lines. In each miRNA-seq dataset, we found an average of more than 500 miRNAs with higher than 5x coverage, and we explored the top five highly expressed miRNAs in each tissue and cell-line. This user-friendly miRmine database has options to retrieve expression profiles of single or multiple miRNAs for a specific tissue or cell-line, either normal or with disease information. Results can be displayed in multiple interactive, graphical and downloadable formats.

Availability and implementation: http://guanlab.ccmb.med.umich.edu/mirmine.

Contact: bharatpa@umich.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1

A workflow of the data source and processing of miRNA-seq data (Color version of this figure is available at Bioinformatics online.)

Fig. 2

Tissue and cell-line specific patterns of all mature miRNAs based on the average expression values (RPM). The hierarchical clustering of both different tissues and cell-lines, and miRNAs are based on the distance metric of Pearson correlation values. In upper panel, all tissues are highlighted with green color whereas cell-lines are highlighted with red color (Color version of this figure is available at Bioinformatics online.)

Fig. 3

A schematic representation of different applications of the miRmine database. All these search options are provided in user-friendly manner (please see section 3.3 for details) (Color version of this figure is available at Bioinformatics online.)

Fig. 4

Different examples of graphical results of the tissue-based search; (a) a box-plot graph for a single miRNA (has-miR-21-5p) query, (b) a column graph for comparing tissue-expression values of four-specific miRNAs, (c) detailed results of experimental information, published literature and expression profiles and (d) downloadable expression profiles of all miRNAs in all tissues (Color version of this figure is available at Bioinformatics online.)