Learning to Discover Regulatory Elements for Gene Expression Prediction

Three Key Components 𝑹 𝒈 -Genomic candidates: Regulatory elements that could interact with the target gene; but may be inactive in certain cell types 𝑹 𝒎 -Measured regions: Detected via epigenomic signals may correlate with expression, but their true target gene is often unknown 𝑹 𝒂𝒈 -Active and causal regulatory elements: Regulatory elements that directly influence target gene expression. These are the true causal drivers we aim to discover Department of Computer Science & Engineering Causal Relationship 𝑿 𝒔𝒆𝒒 ← 𝑹 𝒈 : DNA sequence containing of all regulatory elements 𝑅 𝑔 interacted with target gene and other non-causal regions 𝑹 𝒂𝒈 → 𝒀: Causal active regulatory region that directly affects the gene expression 𝑹 𝒈 ← 𝑹 𝒂𝒈 → 𝑹 𝒎 : Key causal region shared by both DNA and epigenomic signals 𝑹 𝒎 → 𝑿 𝒔𝒊𝒈 : Regulatory elements 𝑅 𝑚 by measurement reflecting active regions in the cell, often showing as peaks in experiments