CircMiMi

CircMiMi constructs circRNA-miRNA-mRNA interaction networks across 18 species (16 animals and 2 plants) from user-specified circRNA junction coordinates to enable analysis of RNA-mediated gene regulation.

Key Features:

• Species Coverage: Supports analysis across 18 species, including 16 animals and 2 plants.
• Network Construction: Builds circRNA-miRNA and miRNA-mRNA interaction networks from user-provided circRNA junction coordinates.
• Integration of Evidence: Integrates computational predictions with experimental data to derive interactions between circRNAs, miRNAs, and mRNAs.
• Back-Splice Junction Analysis: Assesses alignment ambiguity of back-splice junctions to evaluate circRNA identification reliability.
• Reverse Complementary Sequence Investigation: Analyzes reverse complementary sequences flanking circularized exons to examine mechanisms of circRNA formation.
• Implementation: Implemented as a modular Python-based application.

Scientific Applications:

• NeuroCirc-based Network Construction: Constructs circRNA-miRNA-mRNA networks using NeuroCirc human brain circRNA data.
• Autism Spectrum Disorder (ASD) Research: Facilitates identification of regulatory axes by analyzing differentially expressed circRNAs and miRNAs associated with ASD.

Methodology:

Constructs interaction networks via circRNA-miRNA and miRNA-mRNA axes, integrates computational predictions and experimental data, evaluates alignment ambiguity of back-splice junctions, inspects reverse complementary sequences flanking circularized exons, and processes user-defined circRNA junction coordinates.