HHCDB

HHCDB catalogs heterochromatin regions across the human genome to enable analysis of heterochromatin-associated genomic features, functional annotations, and disease-related epigenetic alterations.

Key Features:

• Unified heterochromatin identification pipeline: Heterochromatin regions are systematically identified using a unified pipeline based on specific or combined histone modifications H3K27me3, H3K9me2, and H3K9me3.
• Dataset scope: Contains 42,839,743 heterochromatin regions derived from 578 samples across 241 cell types/cell lines and 92 tissue types.
• Genomic and functional annotations: Provides chromatin location, gene structure, transcripts, distance from transcription start sites, neighboring genes, CpG islands, transposable elements, three-dimensional genomic structures, and functional annotations for each region.
• Single-cell transcriptome integration: Integrates transcriptome data from 73 single cells to identify cell type-specific heterochromatin-related genes.
• Cancer-focused analyses: Supports mining of differential heterochromatin regions in cancers, clinical feature analysis, immune cell infiltration analysis, and construction of drug-target networks for cancer-specific heterochromatin-related genes.

Scientific Applications:

• Epigenetic regulation: Supports study of heterochromatin roles in gene regulation, genome integrity maintenance, and silencing of repetitive DNA elements.
• 3D genomics: Facilitates analysis of three-dimensional genomic structures associated with heterochromatin regions.
• Cancer epigenetics: Enables identification and analysis of cancer-specific differential heterochromatin regions and associated clinical and immune features.
• Drug-target discovery: Supports construction and analysis of drug-target networks for cancer-specific heterochromatin-related genes.
• Cell-type-specific expression analysis: Links heterochromatin regions to transcripts using single-cell transcriptome data to identify cell type-specific heterochromatin-related genes.

Methodology:

Heterochromatin regions were systematically identified using a unified pipeline based on specific or combined histone modifications H3K27me3, H3K9me2, and H3K9me3; regions were derived from 578 samples across 241 cell types/cell lines and 92 tissue types; transcriptome data from 73 single cells were integrated to assess cell type-specific heterochromatin-related genes.