Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Nucleic Acids Res. 2023 Jan 6;51(D1):D306-D314. doi: 10.1093/nar/gkac849.
In mammals, transcriptional factors (TFs) drive gene expression by binding to regulatory elements in a cooperative manner. Deciphering the rules of such cooperation is crucial to obtain a full understanding of cellular homeostasis and development. Although this is a long-standing topic, there is no comprehensive database for biologists to access the syntax of TF binding sites. Here we present TFSyntax (https://tfsyntax.zhaopage.com), a database focusing on the arrangement of TF binding sites. TFSyntax maps the binding motif of 1299 human TFs and 890 mouse TFs across 382 cells and tissues, representing the most comprehensive TF binding map to date. In addition to location, TFSyntax defines motif positional preference, density and colocalization within accessible elements. Powered by a series of functional modules based on web interface, users can freely search, browse, analyze, and download data of interest. With comprehensive characterization of TF binding syntax across distinct tissues and cell types, TFSyntax represents a valuable resource and platform for studying the mechanism of transcriptional regulation and exploring how regulatory DNA variants cause disease.
在哺乳动物中，转录因子（TFs）通过协同结合调控元件来驱动基因表达。解析这种协同作用的规则对于全面了解细胞内稳态和发育至关重要。尽管这是一个长期存在的话题，但生物学家并没有一个全面的数据库来访问 TF 结合位点的语法。在这里，我们介绍 TFSyntax（https://tfsyntax.zhaopage.com），这是一个专注于 TF 结合位点排列的数据库。TFSyntax 绘制了 1299 个人类 TF 和 890 个小鼠 TF 在 382 种细胞和组织中的结合基序，这是迄今为止最全面的 TF 结合图谱。除了位置外，TFSyntax 还定义了可及元件中 motif 位置偏好、密度和共定位。基于一系列基于网络界面的功能模块，用户可以自由搜索、浏览、分析和下载感兴趣的数据。TFSyntax 对不同组织和细胞类型的 TF 结合语法进行了全面描述，是研究转录调控机制和探索调控 DNA 变异如何导致疾病的宝贵资源和平台。
