eccDNA Atlas

eccDNA Atlas curates and integrates experimentally reported and computationally predicted extrachromosomal circular DNAs (eccDNAs and ecDNAs) to support identification, annotation, and analysis of their sequences and disease associations across multiple species.

Key Features:

• Extensive Data Repository: Contains 629,987 manually curated eccDNAs and 8,221 ecDNAs from literature, plus 1,105 ecDNAs predicted by AmpliconArchitect from whole-genome sequencing (WGS) data, spanning 66 diseases, 57 tissues, and 319 cell lines.
• Comprehensive Entry Details: Provides sequence data, associated diseases, reported functional roles, characteristics, and validation strategies for each eccDNA entry.
• Annotation and Analysis Tools: Offers analyses and annotations for oncogenes, typical enhancers, super enhancers, CTCF-binding sites, single nucleotide polymorphisms (SNPs), chromatin accessibility, expression quantitative trait loci (eQTLs), gene expression profiles, survival data, and genome visualization for database and user-defined eccDNAs.
• ecDNA Prediction: Includes ecDNA prediction using AmpliconArchitect applied to WGS datasets.

Scientific Applications:

• Tumorigenesis studies: Investigating the roles of eccDNAs and ecDNAs in tumor initiation, progression, and oncogene amplification.
• Immune response research: Studying potential involvement of eccDNAs in immune-related processes.
• Disease association analyses: Exploring links between eccDNAs and the catalogued 66 diseases across 57 tissues and 319 cell lines.
• Functional genomics: Assessing relationships between eccDNAs and regulatory elements, SNPs, chromatin accessibility, eQTLs, gene expression, and survival outcomes.
• Comparative and cross-species analyses: Enabling comparison of eccDNA characteristics across multiple species.

Methodology:

Data were manually curated from literature and ecDNAs were predicted using AmpliconArchitect on whole-genome sequencing (WGS) datasets.