isomiRdb

isomiRdb provides high-resolution catalogs of microRNA (miRNA) and isomiR expression across human tissues and cell types to enable isoform-resolved analyses of miRNA variation.

Key Features:

• Extensive data collection: Aggregates miRNA expression data from 42,499 human miRNA-seq samples sourced from miRMaster, The Cancer Genome Atlas (TCGA), and the Sequence Read Archive (SRA).
• Uniform processing: Processes raw sequencing reads using sRNAbench to ensure consistent isomiR detection and quantification.
• Comprehensive coverage: Reports 90,483 abundant isomiRs (expression >1 Reads Per Million in at least 1% of samples) across 52 tissues and 188 cell types and provides access to over 3 million detected isomiR variants.
• Flexible querying: Enables queries at the sample, miRNA, or isomiR level to determine presence and frequency of specific miRNAs or isomiRs across samples.
• Visualization support: Provides expression visualizations including violin plots and heatmaps for exploration of complex expression patterns.

Scientific Applications:

• miRNA expression profiling: Enables isoform-resolved quantification of miRNA expression across a large human sample compendium.
• IsomiR discovery and prevalence assessment: Facilitates identification and frequency analysis of known and novel isomiR variants across tissues and cell types.
• Tissue- and cell-type specificity analyses: Supports comparisons of isomiR and miRNA expression patterns across 52 tissues and 188 cell types.
• Disease-associated miRNA studies: Provides isoform-level expression data suitable for investigating miRNA and isomiR roles in disease mechanisms using TCGA and other disease-related datasets.

Methodology:

Raw miRNA-seq reads from miRMaster, TCGA, and SRA were uniformly processed with sRNAbench; abundant isomiRs were defined as those with >1 Reads Per Million in at least 1% of samples within the 42,499-sample compendium.