What is eccDNA Atlas?

   Extrachromosomal circular DNAs (eccDNAs) represent a large category of nonmitochondrial and nonplasmid circular extrachromosomal DNA playing an indispensable role involved in various aspects such as tumorigenesis, immune responses and biomarker, etc. However, characteristic and functions of eccDNAs/ecDNAs are fragmented, hide behind abundant literatures and large amounts of available whole-genome sequencing (WGS) data are unemployed for identification of eccDNAs. Therefore, an integrated repository portal through manually curating eccDNAs from literatures and identifying new eccDNAs from WGS data is essential to further research and understanding the mechanisms and functions of eccDNAs. Here, we developed eccDNA Atlas, a user-friendly database of eccDNAs that aims to provide a high-quality and integrated resource for browsing, searching and analyzing eccDNAs such as sequence, function/characteristic, validation strategies, etc. from multiple species. eccDNA Atlas currently containing 629,987 eccDNAs and 8,221 ecDNAs manually curated from literatures and 1,105 ecDNAs predicted by AmpliconArchitect based on WGS data involved in 66 diseases, 57 tissues and 319 cell lines. Furthermore, abundant annotations and analyzing utilities were provided to explore eccDNA Atlas eccDNAs or user-defined eccDNAs such as oncogenes, typical enhancers, super enhancers, gene expression, survival, genome visualization, etc.

 11/27/2022 eccDNA Atlas v1.05: Add the function of submitting sequence in submit section.

 11/21/2022 eccDNA Atlas v1.05: The analysis of Genome annotation added CTCF binding sites, SNPs, chromatin accessibility, eQTL data.

 11/07/2022 eccDNA Atlas v1.05: Add the function of BLAST.

 07/06/2022 eccDNA Atlas v1.04: Improve the production of database help and contact pages.

 05/11/2022 Complete the construction of the database and go online.

 04/12/2022 eccDNA Atlas v1.03: Update database download,statistics and submit pages.

 03/21/2022 eccDNA Atlas v1.02: Update the page of search section and analysis section.

 02/25/2022 eccDNA Atlas v1.01: Improve and update ecDNA and eccDNA browsing functions.

 02/03/2022 eccDNA Atlas v1.0: Update the library construction process and introduction of the homepage.

 09/01/2021 Conception and design of database.

 07/11/2021 Collect and organize database related data.

Citation: Zhong, T., Wang, W., Liu, H., Zeng, M., Zhao, X., & Guo, Z. (2023). eccDNA Atlas: a comprehensive resource of eccDNA catalog. Briefings in bioinformatics, 24(2), bbad037. https://doi.org/10.1093/bib/bbad037 --------->original article download