SURF

SURF performs integrative analysis of RNA-seq and CLIP-seq data to identify and characterize alternative splicing (AS), alternative transcription initiation (ATI), and alternative polyadenylation (APA) events regulated by RNA-binding proteins (RBPs) and to associate these events with local protein–RNA interactions.

Key Features:

• Integrative analysis: Combines RNA-seq and CLIP-seq datasets to link transcriptome profiles with protein–RNA binding information.
• Regulatory event identification: Identifies and characterizes alternative splicing (AS), alternative transcription initiation (ATI), and alternative polyadenylation (APA) events regulated by individual RBPs.
• Local interaction association: Associates regulatory transcriptional events with local protein–RNA interactions derived from CLIP-seq data.
• Differential event detection: Detects differential alternative transcriptional regulation events across conditions or samples.
• Comprehensive analysis pipeline: Provides a pipeline for large-scale analysis of high-throughput RNA-seq and CLIP-seq collections.

Scientific Applications:

• RBP regulatory role mapping: Elucidates how individual RBPs influence AS, ATI, and APA across the transcriptome.
• Event–binding association: Links differential transcriptional regulation events to RBP binding sites to infer mechanistic relationships.
• ENCODE RBP compendium analysis: Applied to the ENCODE RBP compendium to associate differential transcriptional regulation events with specific protein–RNA interactions.

Methodology:

Integrates CLIP-seq and RNA-seq data within a comprehensive analysis pipeline to detect differential alternative transcriptional regulation events and associate them with local protein–RNA interactions.