IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• IsomiRs are variants of microRNAs (miRNAs) differing in sequence or length.
• Existing tools often fail to identify isomiRs and require bioinformatics expertise.
• IsomiR Window addresses this gap by enabling systematic isomiR analysis.

Purpose of the Study:

• To develop a user-friendly platform for identifying, quantifying, and functionally exploring isomiRs.
• To enable researchers without computational skills to analyze isomiR expression in small RNA-seq datasets.

Main Methods:

• IsomiR Window integrates over ten third-party software tools.
• A novel algorithm detects various isomiR types, including 3'/5' end variants, 3' end tailings, SNPs, and RNA editing.
• The platform is distributed as a Linux virtual machine with all necessary databases and software.

Main Results:

• IsomiR Window processes datasets automatically, generating high-quality interactive figures and tables.
• The tool achieved 100% accuracy in identifying and quantifying different isomiR types using simulated data.
• Analysis of Basal Cell Carcinoma data revealed a novel isomiR variant of miR-183-5p linked to disease pathways.

Conclusions:

• IsomiR Window provides a robust and accessible solution for comprehensive isomiR analysis.
• The platform facilitates the discovery of biologically relevant isomiRs, enhancing understanding of gene regulation and disease.
• The findings underscore the importance of considering isomiRs in molecular and disease research.