isomiRs

isomiRs profiles small non-coding RNAs from sRNA sequencing data, quantifying miRNAs and isomiRs non-redundantly to characterize sequence variants and multi-mapping sRNA species for comparative expression analysis.

Key Features:

• Non-Redundant Quantification: Quantifies all types of small non-coding RNAs non-redundantly to reduce counting redundancy across multi-mapping reads.
• Multi-Mapping Handling: Accounts for sRNA reads that map to multiple loci, enabling inclusion of sRNA species beyond canonical miRNAs.
• Expression Pattern Extraction: Extracts expression patterns across biologically defined groups for comparative analyses.
• IsomiR Profiling: Characterizes miRNA sequence variants (isomiRs) to capture miRNA diversity and sequence heterogeneity.
• Clustering and Differential Expression: Identifies clusters of co-expressed sRNAs (including those mapping to tRNAs) and performs differential expression analysis between conditions.

Scientific Applications:

• Parkinson's disease sRNA analysis: Applied to post-mortem brain samples to identify sRNA clusters that distinguish premotor and motor Parkinson's disease cases from controls.
• Discovery of disease-associated sRNA patterns: Used to uncover sRNA expression alterations and early pathogenic perturbations across diseases and disease stages.

Methodology:

Processes sRNA sequencing data with non-redundant quantification, extracts expression patterns across defined groups, profiles isomiRs, and identifies co-expressed sRNA clusters and differential expression.