PRAS

PRAS predicts functional mRNA targets of RNA-binding proteins by integrating CLIP-seq binding peak intensities and positions to infer protein–RNA association strength.

Key Features:

• Integration of Binding Peak Data: Integrates both intensities and positions of CLIP-seq-derived binding peaks to predict functional mRNA targets.
• Superior Predictive Capability: Demonstrated superior performance over existing methods for predicting functional targets of CELF (CUGBP, ELAV-like factor) RBPs in mouse brain and muscle tissues.
• Broad Applicability: Applicable to any RBP with available CLIP-seq data, including enhanced CLIP (eCLIP) datasets.
• Validation Across Species and Conditions: Validated using eCLIP datasets involving 37 RNA decay-related RBPs in two human cell lines.

Scientific Applications:

• Post-transcriptional Regulation Studies: Predicts functional mRNA targets of RBPs to elucidate mechanisms of post-transcriptional regulation.
• Comparative Analysis Across Tissues: Enables comparison of RBP functional targets across tissues or conditions, as illustrated for CELF proteins in mouse brain and muscle.
• Human Cell Line Research: Supports analysis of RNA decay-related RBPs using eCLIP datasets from human cell lines.

Methodology:

Combines quantitative intensities and positional information of CLIP-seq/eCLIP-derived binding peaks within the transcriptome to predict which mRNAs are functionally influenced by specific RBPs.