BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation.
Federal Research Center for Information and Computational Technologies, Novosibirsk 630090, Russian Federation.
Nucleic Acids Res. 2021 Jan 8;49(D1):D104-D111. doi: 10.1093/nar/gkaa1057.
The Gene Transcription Regulation Database (GTRD; http://gtrd.biouml.org/) contains uniformly annotated and processed NGS data related to gene transcription regulation: ChIP-seq, ChIP-exo, DNase-seq, MNase-seq, ATAC-seq and RNA-seq. With the latest release, the database has reached a new level of data integration. All cell types (cell lines and tissues) presented in the GTRD were arranged into a dictionary and linked with different ontologies (BRENDA, Cell Ontology, Uberon, Cellosaurus and Experimental Factor Ontology) and with related experiments in specialized databases on transcription regulation (FANTOM5, ENCODE and GTEx). The updated version of the GTRD provides an integrated view of transcription regulation through a dedicated web interface with advanced browsing and search capabilities, an integrated genome browser, and table reports by cell types, transcription factors, and genes of interest.
基因转录调控数据库（GTRD；http://gtrd.biouml.org/）包含与基因转录调控相关的经过统一注释和处理的 NGS 数据：ChIP-seq、ChIP-exo、DNase-seq、MNase-seq、ATAC-seq 和 RNA-seq。在最新版本中，该数据库达到了新的数据集成水平。GTRD 中呈现的所有细胞类型（细胞系和组织）都被组织成一个字典，并与不同的本体论（BRENDA、细胞本体论、Uberon、Cellosaurus 和实验因子本体论）以及转录调控的专门数据库中的相关实验（FANTOM5、ENCODE 和 GTEx）相关联。GTRD 的更新版本通过专用的网络界面提供转录调控的综合视图，该界面具有高级浏览和搜索功能、集成基因组浏览器以及按细胞类型、转录因子和感兴趣的基因的表格报告。
