ReCirc

ReCirc predicts circular RNA (circRNA) expression and facilitates functional annotation by reannotating microarray probes from non-circRNA microarrays to enable circRNA profiling from existing microarray datasets.

Key Features:

• Probe Reannotation: Aligns microarray probe sequences to circRNA body sequences and back-spliced junction sequences to identify candidate circRNAs.
• Data Utilization: Transforms non-circRNA microarray data into circRNA profiles, exemplified by reannotating 39,818 probe set–circRNA pairs involving 5,388 circRNAs on an Affymetrix human exon array.
• Validation against RNase R+ RNA-seq: Compares reannotated circRNAs with RNase R-resistant circRNAs identified by RNA-seq-based methods such as find_circ in the HeLa cell line, with better detection for higher-expression circRNAs.
• Cross-Platform Consistency: Compares circRNA expression profiles with the Agilent-069978 Arraystar Human CircRNA microarray and reports consistent expression patterns in identical tissues.
• Expression Variation Analysis: Computes circRNA expression variation across multiple cell lines and compares performance with find_circ; molecular verification in HeLaS3 confirmed 5 of 9 randomly selected circRNAs.
• Functional Insights: Performs functional analysis of identified circRNAs across four cancer types to assess potential roles as diagnostic and prognostic biomarkers.

Scientific Applications:

• CircRNA discovery from microarrays: Repurposes existing non-circRNA microarray datasets to identify and quantify circRNAs across tissues and cell lines.
• Cross-platform comparison: Enables comparative evaluation of circRNA profiles between microarray reannotation results, RNA-seq-based detection (e.g., find_circ), and dedicated circRNA microarrays (Agilent-069978 Arraystar).
• Expression variation studies: Facilitates analysis of circRNA expression variation across multiple cell lines.
• Cancer biomarker analysis: Supports functional and biomarker analyses of circRNAs across four different cancer types for diagnostic and prognostic assessment.

Methodology:

ReCirc reannotates probes by sequence alignment of microarray probe sequences to circRNA body and back-spliced junction sequences, compares reannotated circRNAs to RNase R-resistant circRNAs identified by RNA-seq methods such as find_circ and to Agilent-069978 Arraystar Human CircRNA microarray profiles, and computes circRNA expression variation across cell lines.