CIRI

CIRI de novo identifies and reconstructs full-length circular RNAs (circRNAs) and quantifies isoform-level expression from transcriptome data.

Key Features:

• Reverse Overlap (RO) Feature: Detects low-abundance circRNAs using the reverse overlap (RO) signal, increasing sensitivity compared to back-splice junction (BSJ)-based detection.
• Combination of RO and BSJ Features: Integrates reverse overlap (RO) and back-splice junction (BSJ) features to reconstruct full-length circRNAs and characterize isoforms.
• Isoform-Level Quantification: Provides quantitative estimates at the isoform level to enable differential expression analyses with isoform resolution.
• Application in Differential Expression Analysis: Has been evaluated on human liver tumor and normal tissue samples to distinguish BSJ-level and isoform-level differential expression.

Scientific Applications:

• circRNA discovery and isoform characterization: Enables de novo identification and full-length reconstruction of circRNAs and their isoforms from transcriptome data.
• Cancer-related differential expression: Supports isoform-level differential expression studies, exemplified by human liver tumor versus normal tissue comparisons.

Methodology:

Combines reverse overlap (RO) and back-splice junction (BSJ) features in an algorithmic approach to reconstruct full-length circRNA sequences from transcriptome data.