functional-screen-analysislisted

# Analyze ENCODE Functional Genomics Screens ## When to Use - User wants to find or analyze CRISPR screen, MPRA, or STARR-seq data from ENCODE - User asks about "functional screens", "CRISPR perturbation", "reporter assay", or "enhancer validation" - User needs to identify functionally validated regulatory elements from screen results - User wants to integrate screen results with epigenomic annotations (ChIP-seq, ATAC-seq peaks) - Example queries: "find CRISPR screen data in ENCODE", "analyze MPRA results for enhancer activity", "which regulatory elements have functional validation?" Discover and interpret functional validation data from CRISPR screens, MPRA (Massively Parallel Reporter Assays), and STARR-seq experiments in the ENCODE catalog. These assays directly test whether candidate regulatory elements have functional activity, complementing the correlative evidence from ChIP-seq, ATAC-seq, and Hi-C. ## Scientific Rationale **The question**: "Which of the candidate regulatory elements identified by ENCODE actually have functional activity, and what genes do they regulate?" The central challenge in regulatory genomics is that biochemical signatures (histone marks, chromatin accessibility, TF binding) are correlative — they identify *candidate* regulatory elements but cannot prove function. ENCODE Phase 4 addressed this gap by investing heavily in functional characterization: large-scale CRISPR perturbation screens, MPRA experiments testing thousands of candidate ele