Abstract

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.

中文翻译：

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GTRD：转录调控的综合观点

摘要

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统一注释和处理的 NGS 数据：ChIP-seq、ChIP-exo、DNase-seq、MNase-seq、ATAC- seq 和 RNA 测序。在最新版本中，数据库已达到数据集成的新水平。GTRD 中呈现的所有细胞类型（细胞系和组织）都被整理成字典，并与不同的本体（BRENDA、细胞本体、Uberon、Cellosaurus 和实验因子本体）以及转录调控专业数据库（FANTOM5、编码和 GTEx）。GTRD 的更新版本通过具有高级浏览和搜索功能的专用网络界面、集成基因组浏览器以及按细胞类型、转录因子和感兴趣基因列出的表格报告，提供了转录调控的综合视图。