epigenome-profiling

What problem does it solve?

This Skill enables comprehensive characterization of the epigenomic landscape of biosamples by integrating multiple data types and informatics methods.

Core Features & Use Cases

• Data Collection: Identifies available histone modifications, chromatin accessibility, DNA methylation, transcription, and 3D genome data from ENCODE for targeted biosamples.
• Chromatin State Annotation: Uses ChromHMM to segment the genome into functional states based on histone mark combinations, aiding in identifying promoters, enhancers, and repressed regions.
• Profile Integration: Facilitates the combination of multi-omic datasets to interpret regulatory mechanisms underlying gene expression and cellular identity.
• Use Case: A researcher profiles pancreatic tissue, gathers required data, and annotates chromatin states to link epigenetic marks with regulatory elements.

Quick Start

Collect ENCODE experiments for your tissue of interest, assemble core histone marks, chromatin accessibility, and gene expression data, then analyze the combined epigenome through chromatin state segmentation.