CircIMPACT: An R Package to Explore Circular RNA Impact on Gene Expression and Pathways

Area of Science:

• Bioinformatics
• Molecular Biology
• Genomics

Background:

• Circular RNAs (circRNAs) are key regulators of cellular processes.
• Dysregulated circRNAs are linked to human diseases, including cancer, by affecting gene expression and signaling pathways.
• Investigating circRNA functions is crucial due to their aberrant expression in disease.

Purpose of the Study:

• To develop CircIMPACT, a bioinformatics tool for integrative analysis of circRNA and gene expression data.
• To identify and visualize genes whose expression correlates with circRNA expression changes.
• To highlight potential circRNA-governed regulatory axes for experimental prioritization.

Main Methods:

• Development of the CircIMPACT bioinformatics tool.
• Integrative analysis of circRNA and gene expression datasets.
• Case study using bladder cancer RNA-seq data.

Main Results:

• CircIMPACT successfully identified genes whose expression varies with circRNA levels.
• The tool detected the circHIPK3-miR558-HPSE regulatory axis in bladder cancer data.
• Demonstrated the ability to highlight potential circRNA-mediated regulatory mechanisms.

Conclusions:

• CircIMPACT facilitates the functional investigation of circRNAs by integrating expression data.
• The tool aids in discovering circRNA-driven regulatory networks relevant to diseases like cancer.
• CircIMPACT is a valuable resource for prioritizing circRNAs for experimental validation.