Protein-Mediated Regulatory Community Analysis from ChIA-PET

1. Overview

Main steps include:

• Refer to the Inputs & Outputs section to check available inputs and design the output structure.
• Standardize the information contained in the BED format peak file.
• Build a chromatin interaction network where:
  • nodes = protein binding sites (peaks)
  • edges = protein-mediated loops.
• Detect regulatory communities (3D modules) using graph clustering.
• Prioritize hub anchors using network centrality.
• Visualize the largest regulatory communities.

Tools called in this skill: