ATACdb 2.0:一个全面的人类和小鼠染色质可访问性数据库
Qiao-Li Fang1,2, Feng-Cui Qian1,3, Zheng-Min Yu2
1The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
Nucleic acids research
|November 17, 2025
概括
ATACdb 2.0 通过扩展人类和小鼠样本来增强染色质可访问性数据,为基因调节研究提供更丰富的注释和改进的分析工具.
科学领域:
- 基因组学和表观基因组学
- 生物信息学和计算生物学
背景情况:
- 染色体可访问性是转录活动的关键指标,对于理解基因调节,细胞功能和疾病病原体至关重要.
- 现有的染色体可访问性数据资源需要扩大规模和注释多样性.
研究的目的:
- 引入ATACdb 2.0,一个显著改进和扩展的染色体可访问性数据库.
- 增强染色体可访问性信息的实用性,用于基因调节和疾病机制研究.
主要方法:
- 通过结合新的小鼠数据和额外的人类样本来扩展数据库.
- 从scATAC-seq数据生成伪批量ATAC-seq配置文件,以增加细胞类型的表示.
- 综合综合的遗传和表观遗传注释,包括静音器,CpG岛屿,meQTL,基因素修饰,eRNA,TF和TcoF.
主要成果:
- ATACdb 2.0包含来自4,031个人类样本的超过3.19亿个染色质可访问区域 (CAR) 和来自1,273个小鼠样本的超过7500万个CAR.
- 该数据库现在提供了丰富的注释和先进的分析功能,如"通过SNP搜索"和"基因组区域丰富分析".
- 引入了优化的目标基因识别方法和额外的数据质量控制指标.
结论:
- ATACdb 2.0代表了染色体可访问性资源的重大进步,提供了更大的数据量,多样性和分析能力.
- 增强的资源有助于更全面,更可靠地探索染色体可访问性在基因调节和疾病中的作用.
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