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eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA.

Jin-Hao Zhang1, Chang-Lin Yang1, Chang-Yuan Ren1

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Molecular Biology and Evolution
|September 19, 2025
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Extrachromosomal circular DNA (eccDNA) plays a key role in tumorigenesis. The new eccDNABase resource catalogs over 1.8 million eccDNA-disease associations, aiding research into eccDNA

Keywords:
databasediseaseeccDNA

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Extrachromosomal circular DNA (eccDNA) are small, circular DNA molecules found in eukaryotes.
  • eccDNAs are prevalent in human tissues and body fluids, implicated in tumorigenesis and poor clinical outcomes.

Purpose of the Study:

  • To develop a comprehensive, curated database for eccDNA research.
  • To systematically catalog eccDNA-disease associations across multiple species and tissues.

Main Methods:

  • Developed eccDNABase, a database integrating eccDNA data.
  • Cataloged eccDNA entries, species, diseases, and associated information.
  • Included details on chromosomal localization, gene overlap, and detection methods.

Main Results:

  • eccDNABase contains 1,875,452 eccDNA-disease associations.
  • The database includes 8,398 eccDNA entries across nine species and 63 diseases.
  • Detailed information on eccDNA characteristics and disease links is provided.

Conclusions:

  • eccDNABase is a valuable resource for eccDNA research.
  • Facilitates deeper insights into the role of eccDNA in health and disease.
  • Provides a platform for basic and translational research.