eccDNA Atlas

Extrachromosomal circular DNAs (eccDNAs) represent a large category of nonmitochondrial and nonplasmid circular extrachromosomal DNA, and eccDNAs play an indispensable role involved in various aspects such as tumorigenesis, immune responses and biomarker, etc. 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.染色体外环状DNA（extrachromosomal circular DNAs, eccDNAs）是一类广泛分布的非线粒体、非质粒型环状染色体外DNA，在肿瘤发生、免疫应答及生物标志物开发等诸多领域发挥着不可或缺的关键作用。本研究开发了eccDNA Atlas——一款易用的eccDNA数据库，旨在为多物种的eccDNA数据提供高质量、一体化的浏览、检索与分析资源，涵盖序列、功能/特性、验证策略等多个维度。目前，eccDNA Atlas共收录629,987条eccDNA、8,221条经文献手动整理注释的染色体外DNA（extrachromosomal DNA, ecDNA），以及基于全基因组测序（Whole Genome Sequencing, WGS）数据通过AmpliconArchitect预测得到的1,105条ecDNA，相关数据覆盖66种疾病、57种组织及319个细胞系。此外，该数据库还提供了丰富的注释信息与分析工具，支持用户对数据库内置eccDNA或自定义eccDNA开展探索分析，涵盖癌基因、典型增强子、超级增强子、基因表达、生存分析、基因组可视化等多个方向。

搜集汇总

背景与挑战

背景概述

eccDNA Atlas是一个综合性的eccDNAs/ecDNAs数据门户，涵盖多个物种的健康和疾病相关数据。该数据库通过整合文献手动整理和全基因组测序数据预测，目前包含超过60万个eccDNAs记录，涉及66种疾病、57种组织和319种细胞系，并提供丰富的注释和分析工具，如序列浏览、功能探索和基因组可视化，以支持eccDNA的机制和功能研究。