Build comprehensive epigenomic tissue profiles

Profile epigenetic modifications across genome (chromatin marks, accessibility, 3D structure)

Cancer or developmental biology where multi-mark epigenome profiles reveal tumor states or differentiation trajectories better than single assay.

• · ChIP-seq peaks (BED)
• · ATAC-seq footprints (BED)
• · Hi-C contact matrix
• · methylation (BED graph)

• · chromatin state map (Roadmap states 1-18)
• · enrichment heatmap (marks vs regions)
• · 3D TAD calls + boundary strength

• · Roadmap Epigenomics reference (111 reference epigenomes)
• · ChromHMM (hidden Markov model)
• · HiCstuff (3D structure tools)

Multiple mark types (H3K4me3, H3K27ac, H3K27me3) present for state calling; cell type matches Roadmap

• · single mark alone insufficient for state assignment → merge multiple marks first
• · cell-type-specific states may not match Roadmap exactly
• · imbalanced mark coverage → HMM bias

• · Roadmap reference (111 epigenomes, tissue-specific)
• · ChromHMM integration (Markov model for state calling)
• · 3D structure + 1D marks for mechanistic insight