eccDNAdb

eccDNAdb catalogs extrachromosomal circular DNAs (eccDNAs) identified in human cancers to enable analysis of their roles in oncogene amplification and tumor progression.

Key Features:

• Extensive Data Collection: Integrates whole-genome sequencing (WGS) data from public repositories with manually curated literature to compile eccDNA entries.
• Diverse Sample Inclusion: Contains 1270 eccDNAs identified in 480 samples across 42 cancer types from analysis of 3395 tumor samples including patient tissues, patient-derived xenografts, and cancer cell lines.
• Gene Annotation: Provides a dataset comprising 54,901 annotated eccDNA genes for gene-level analyses.
• Integrated Data Layers: Incorporates gene expression data, clinical information, and chromatin accessibility data from TCGA and CCLE for multifaceted analyses.

Scientific Applications:

• Mechanistic Studies: Investigate how eccDNAs contribute to oncogene amplification and tumor progression in human cancers.
• Cross-cancer Comparative Analysis: Compare eccDNA profiles across 42 cancer types and 3395 tumor samples to identify recurrent eccDNA events.
• Biomarker and Target Assessment: Correlate eccDNA presence and eccDNA-encoded gene expression with clinical data to evaluate potential biomarkers and therapeutic targets.

Methodology:

Integration of whole-genome sequencing (WGS) data from public repositories with manual literature curation; integration of gene expression, clinical, and chromatin accessibility data from TCGA and CCLE; annotation of eccDNA genes yielding 54,901 annotated eccDNA genes.