miRSwitch

miRSwitch detects and analyzes miRNA arm shifts from pre-processed small non-coding RNA sequencing (sncRNA-seq) data to quantify changes in mature miRNA arm usage across conditions and species.

Key Features:

• Species-Independent Analysis: Evaluates pre-processed sncRNA-seq data across species and accepts expression matrices as well as miRDeep2, miRMaster, and sRNAbench output files.
• Dynamic Group Comparisons: Performs group comparisons based on user-provided annotations to investigate changes in mature miRNA distributions from the same precursor across conditions or tissues.
• Customizable Parameters: Provides adjustable analysis parameters along a continuum from highly specific to very sensitive settings.
• Human Reference Map Integration: Compares detected arm shifts against a human reference map of pre-computed arm shift frequencies derived from 46 tissues and 30,521 samples.
• Comprehensive Visualizations: Generates detailed visual representations of arm shift and miRNA arm usage results.

Scientific Applications:

• miRNA dynamics studies: Enables investigation of miRNA arm selection and dynamics across conditions and tissues.
• Alzheimer's disease biomarker analysis: Has been applied to identify novel arm shifts in Alzheimer's disease biomarker datasets to provide insights into regulatory mechanisms.
• Comparative cross-species tissue studies: Facilitates comparative analyses between tissues of different species, exemplified by analyses involving Homo sapiens and Mus musculus to study conservation and divergence of miRNA regulation.

Methodology:

Processes pre-processed sncRNA-seq expression matrices or outputs from miRDeep2, miRMaster, and sRNAbench; performs group comparisons using user-provided annotations; compares results to a human reference map of pre-computed arm shift frequencies derived from 46 tissues and 30,521 samples; allows parameter adjustment along a specificity–sensitivity continuum and produces visualizations.