miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data

Area of Science:

• Bioinformatics
• Genomics
• Molecular Biology

Background:

• Computational analysis of microRNA (miR) sequencing data is crucial but challenging for biologists lacking extensive bioinformatics expertise.
• Existing tools often fail to fully address the complexity of miR isoforms (isomiRs) and their differential expression (DE).

Purpose of the Study:

• To present miRGalaxy, a user-friendly, Galaxy-based framework for comprehensive microRNA and isomiR analysis.
• To provide tools for detailed examination of isomiR structure, complexity, and differential expression.
• To facilitate the identification and annotation of differentially expressed miRs and isomiRs in biological samples.

Main Methods:

• Development of a modular, accessible, and user-friendly framework integrated into the Galaxy platform.
• Implementation of workflows for analyzing small RNA (sRNA)-seq data, focusing on isomiRs.
• Provision of customizable options for advanced users and automated report generation with visualizations.
• Accessibility via Docker image or Galaxy Toolshed installation.

Main Results:

• miRGalaxy offers comprehensive analysis of miRs and isomiRs, including their complex structures and differential expression.
• The framework supports in-depth analysis of sRNA-seq data from various biofluids like milk and plasma.
• Generated analysis reports summarize significant findings through charts and visualizations.

Conclusions:

• miRGalaxy empowers biologists to conduct sophisticated isomiR-ome analyses without deep bioinformatics knowledge.
• The framework enhances the discovery of potential diagnostic biomarkers from miR and isomiR expression profiles.
• miRGalaxy facilitates the exploration of the miR repertoire for liquid biopsy applications.