HiChIPdb

HiChIPdb catalogs HiChIP-derived chromatin interactions to support analysis of three-dimensional genome architecture and gene regulation.

Key Features:

• HiChIP-based profiling: Interactions are derived from HiChIP chromatin conformation capture data that profiles regulatory marks such as H3K27ac and structural factors such as cohesin.
• Dataset scale: The database contains approximately 262 million annotated HiChIP interactions aggregated from over 200 HiChIP samples spanning 108 distinct cell types.
• Hierarchical categorization: Interactions are organized using a standardized hierarchy of organ, tissue, and cell line classifications.
• Interaction annotations: Each interaction is annotated with associated regulatory genes and GWAS Catalog single nucleotide polymorphisms (SNPs).
• Unified pipeline: A unified pipeline maps functional interactions across diverse cell types and tissues at different resolutions, ensuring consistent aggregation, preprocessing, and analysis.

Scientific Applications:

• 3D genome and gene regulation: Analysis of chromatin interactions to investigate three-dimensional genome architecture and its role in gene regulation, including processes such as cell differentiation and tissue homeostasis.
• Disease variant interpretation: Linking GWAS Catalog SNPs to regulatory interactions and target genes to prioritize candidate variants and infer potential disease mechanisms.
• Comparative cell-type analysis: Cross-cell-type and tissue comparisons of interaction patterns using data from 108 distinct cell types to identify context-specific regulatory interactions.

Methodology:

Aggregation of >200 HiChIP samples using HiChIP technology; standardized hierarchical categorization by organ, tissue, and cell line; a unified pipeline for mapping functional interactions at multiple resolutions; annotation of interactions with regulatory genes and GWAS Catalog SNPs; preprocessing and analysis of aggregated data.