RBP-Maps

RBP-Maps generates splicing regulatory maps by integrating in vivo RBP binding data (CLIP/eCLIP) with alternative splicing events from RNA-seq or microarray to reveal position-specific effects of RBPs on splice site selection and exon inclusion.

Key Features:

• Integration of datasets: Combines in vivo RBP binding data from CLIP (including eCLIP) with alternative splicing calls derived from RNA-seq or microarray.
• Splicing map construction: Produces splicing regulatory maps by computing CLIP signal relative to a merged meta-exon to assess positional regulatory patterns.
• Signal representations: Supports multiple CLIP signal metrics, including peak-based and read-density-based representations.
• Crosslink resolution options: Allows analysis using whole-reads versus single-nucleotide candidate crosslink positions to vary positional resolution.
• Reference datasets: Demonstrated with example eCLIP data from 150 RBPs profiled by the ENCODE consortium for comparative analyses.
• Focus on alternative splicing regulation: Targets analysis of how RBPs influence exon inclusion and splice site selection across genomic contexts.

Scientific Applications:

• Position-specific RBP regulation: Identify and interpret location-dependent effects of RBP binding on alternative splicing events.
• Comparative RBP analysis: Compare splicing regulatory patterns across multiple RBPs using ENCODE eCLIP data for up to 150 proteins.
• Methodological impact assessment: Evaluate how choices such as peak versus read-density metrics or whole-read versus single-nucleotide crosslink positions affect splicing map interpretation.
• Integration of transcriptomic and CLIP data: Link RNA-seq or microarray-derived splicing changes to observed CLIP binding distributions.

Methodology:

Integrate CLIP/eCLIP binding data with alternative splicing events from RNA-seq or microarray, compute CLIP signal relative to a merged meta-exon to generate splicing maps, and compare analyses using peak versus read-density metrics and whole-read versus single-nucleotide candidate crosslink positions using example ENCODE eCLIP data from 150 RBPs.