eccBase

eccBase provides a curated database of extrachromosomal circular DNAs (eccDNAs) from Homo sapiens and Mus musculus to support research on eccDNA composition, genomic origins, regulatory and epigenetic annotations, and associations with cancer and tissue specificity.

Key Features:

• Extensive Data Collection: Contains 754,391 human eccDNA entries (samples from 50 cancer tissue/cell line types and five healthy tissue types) and 481,381 mouse eccDNA entries (samples from 13 healthy tissues or cell lines).
• Detailed Annotation: Each eccDNA is annotated with basic information, genomic composition, regulatory elements, epigenetic modifications, and associated raw data.
• BLAST-based Similarity Alignment: Integrated BLAST functionality is provided for sequence similarity searches and comparative genomic analyses.
• Comparative Analysis Findings: Comparative analyses indicate cancer-associated eccDNAs are primarily composed of nucleosomes, originate from gene-dense regions, and display strong tissue-specific patterns.

Scientific Applications:

• Cancer Research: Enables identification and analysis of eccDNAs associated with diverse cancer types for studies of cancer progression and molecular associations.
• Mechanistic Studies: Supports computational and experimental investigations into eccDNA roles in gene regulation and cellular function.
• Liquid Biopsy Development: Provides data for developing algorithms and assays for non-invasive diagnostic and monitoring approaches using eccDNA.
• Tissue Differentiation Studies: Facilitates analysis of tissue-specific eccDNA patterns to investigate roles in cell function and differentiation.

Methodology:

Entries were annotated with genomic composition, regulatory elements, epigenetic modifications and linked raw data; BLAST-based similarity alignment and comparative analyses were used to assess eccDNA composition, genomic origins, and tissue specificity.