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EXPRESSO:一个多层的数据库来探索多层的3D基因组组织

Liuyang Cai¹, Jun Qiao¹, Ruixin Zhou¹

¹Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China.

Nucleic acids research

|November 5, 2024

概括

EXPRESSO数据库整合了多omics数据,以可视化人类组织的3D基因组组织和基因调节. 这一资源有助于研究人员了解基因组架构.

科学领域:

基因组学就是基因组学.
表观遗传学在表观遗传学中,表观遗传学是指表观遗传学.
生物信息学是一种生物信息学.

背景情况:

三维 (3D) 基因组组织对于基因调节至关重要.
了解3D基因组结构和基因表达之间的相互作用需要集成的多omics数据.

研究的目的:

介绍EXPRESSO,一个新的多omics数据库,用于探索和可视化46个人类组织的3D基因组特征.
为研究3D基因组架构和转录调节之间的关系提供一个全面的资源.

主要方法:

从匹配的生物样本中整合了1360个3D基因组数据集 (Hi-C,HiChIP,ChIA-PET) 和842个1D基因组/转录基因组数据集 (ChIP-seq,ATAC-seq,RNA-seq).
开发一个用户友好的界面,用于数据探索,可视化和下载.
实现RESTful API用于程序访问和基于Web的应用程序,以将基因组特征与基因表达相关联.

主要成果:

EXPRESSO提供各种3D基因组特征类型,包括隔间,接触矩阵,域,条纹和色素环.
该数据库提供先进的可视化工具和Web应用程序,用于探索多层3D基因组数据.
通过RESTful API进行程序访问,可以进行高级数据检索和分析.

结论:

埃克斯普雷索 (EXPRESSO) 作为一个重要的,自由可用的资源,供研究界深入了解3D基因组架构.
该数据库有助于研究3D基因组组织对人类健康和疾病的影响.
通过EXPRESSO,可以全面探索空间基因组组织和基因调节之间的关系.

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