circRIP

circRIP identifies interactions between circular RNAs (circRNAs) and RNA-binding proteins (RBPs) from RIP-Seq and eCLIP data for genome-wide mapping of RBP–circRNA associations.

Key Features:

• Algorithmic innovation: Employs a unique algorithm specifically tailored to detect circRNA–RBP interactions from RIP-Seq datasets.
• Sensitivity and specificity: Demonstrated high sensitivity and specificity based on rigorous simulation testing.
• Support for multiple data types: Analyzes RIP-Seq and enhanced cross-linking immunoprecipitation (eCLIP) datasets.
• Extensive interaction mapping: Identified 95 IGF2BP3-binding circRNAs from an IGF2BP3 RIP-Seq dataset and mapped 2,823 and 1,333 circRNAs binding to more than 100 RBPs in K562 and HepG2 cell lines, respectively, using eCLIP data.

Scientific Applications:

• Functional characterization of circRNAs: Enables identification of circRNAs that interact with RBPs to support studies of circRNA function.
• Regulatory mechanism and disease research: Facilitates investigation of RBP–circRNA networks relevant to gene expression regulation and potential roles of circRNAs in biological processes and diseases.

Methodology:

Analyzes RIP-Seq and eCLIP datasets to systematically identify RBP–circRNA interactions and employs simulation testing to assess sensitivity and specificity.