CATA

CATA catalogs chromatin accessibility regions (CARs) from ATAC-seq tumor samples and annotates them with genomic and clinical features to support cancer epigenetics research.

Key Features:

• Dataset: 2,991,163 chromatin accessible regions identified across 410 tumor samples spanning 24 distinct types of cancers.
• Data source: CARs derived from ATAC-seq data from tumor samples.
• Clinical annotation: CARs are linked to relevant clinical information for the tumor samples.
• Transcription factor binding site predictions: Predicted transcription factor binding sites associated with CARs are provided.
• SNP annotations: Single nucleotide polymorphisms (SNPs) are annotated relative to CARs.
• Risk-associated SNPs: Risk-associated SNPs are annotated in the context of CARs.
• Linkage disequilibrium SNPs: Linkage disequilibrium (LD) SNP annotations are included.
• eQTLs: Expression quantitative trait loci (eQTL) annotations are integrated with CARs.
• Copy number variations (CNVs): CNV annotations are associated with CAR regions.
• Single nucleotide variants (SNVs): SNV annotations are provided for CARs.
• Enhancer annotations: Enhancer regions are annotated relative to CARs.
• 450K methylation sites: 450K methylation site annotations are integrated with CARs.

Scientific Applications:

• Biomarker discovery: Identification of chromatin-accessibility–based biomarkers for cancer studies.
• Therapeutic target prioritization: Prioritization of candidate therapeutic targets by integrating CARs with genetic and epigenetic annotations.
• Gene regulation analysis: Investigation of cancer-specific gene regulation mechanisms through annotated CARs and TF binding predictions.
• Functional peak analysis: Exploration of potential functional roles of ATAC-seq peaks within the tumor microenvironment.
• Oncogenesis and progression studies: Examination of epigenetic contributions to oncogenesis and tumor progression using integrated annotations.

Methodology:

Annotation of CARs derived from ATAC-seq tumor samples with clinical information, predicted transcription factor binding sites, SNPs (including risk-associated and LD SNPs), eQTLs, CNVs, SNVs, enhancer regions, and 450K methylation sites.