ChIP-Atlas

ChIP-Atlas aggregates and indexes public ChIP-seq, DNase-seq, ATAC-seq, and whole-genome bisulfite sequencing datasets aligned to reference genome assemblies to enable epigenomic data mining and analysis of transcriptional regulation across six model organisms.

Key Features:

• Data Integration: Consolidates public ChIP-seq, DNase-seq, ATAC-seq, and whole-genome bisulfite sequencing datasets for combined epigenomic analysis.
• Genome Alignment: Aligns datasets to the latest reference genome assemblies for each supported organism.
• Supported Organisms: Includes datasets from human, mouse, rat, fruit fly, nematode, and budding yeast.
• Visualization: Provides the Peak Browser tool and a genome browser view to visualize peaks, chromatin accessibility, DNA methylation, and protein–DNA interactions at specific genomic loci.
• Enrichment Analysis Tool: Performs enrichment analyses across gene sets or genomic regions to identify significant epigenomic associations, including examples such as inflammatory bowel disease–related SNPs associated with neutrophil hypo-methylation.

Scientific Applications:

• Epigenomics: Comparative and integrative analysis of chromatin states, DNA methylation, and protein–DNA binding across datasets and organisms.
• Transcriptional Regulation: Investigation of regulatory element activity and transcription factor binding patterns underlying gene expression control.
• Disease Association Studies: Mapping and characterization of disease-associated variants and their epigenomic correlates, such as SNP–methylation relationships relevant to inflammatory bowel disease.

Methodology:

Comprehensive integration of public high-throughput sequencing datasets (ChIP-seq, DNase-seq, ATAC-seq, whole-genome bisulfite sequencing) and alignment of those datasets to the latest genome assemblies for each model organism.