CIRCexplorer3

CIRCexplorer3 quantifies and compares circular RNA (circRNA) and linear RNA expression from ribosomal-RNA depleted RNA sequencing datasets to enable genome-wide evaluation of circRNA versus cognate linear RNA expression.

Key Features:

• CIRCexplorer3-CLEAR: An implementation tailored for direct, genome-wide comparison of circRNA and linear RNA expression.
• FPB metric: Quantifies expression using fragments per billion mapped bases (FPB) for both circRNAs and linear RNAs.
• Fragment mapping: Maps RNA-seq fragments to back-splicing junction (BSJ) sites for circRNAs and splicing junction (SJ) sites for linear RNAs.
• CIRCscore: Calculates CIRCscore as the ratio FPB_circ / FPB_linear to measure circRNA expression relative to its linear counterpart.
• Candidate prioritization: Identifies highly expressed circRNAs with low cognate linear RNA expression as candidates for further study.
• Dataset compatibility: Operates on ribosomal-RNA depleted RNA sequencing datasets.

Scientific Applications:

• Differential expression analysis: Enables comparison of expression patterns between circRNAs and their cognate linear RNAs at the same gene loci.
• Functional candidate selection: Prioritizes circRNAs for functional studies based on relative expression (CIRCscore) and low linear transcript levels.
• Regulatory role investigation: Supports bioinformatics and molecular biology studies into the regulatory potential of circRNAs in biological processes and diseases.

Methodology:

Quantifies circRNA and linear RNA expression by mapping RNA-seq fragments to BSJ (for circRNAs) or SJ (for linear RNAs), computes fragments per billion mapped bases (FPB) for each, and derives CIRCscore as FPB_circ / FPB_linear.