School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu City, Sichuan Province, P.R. China.
Database (Oxford). 2019 Jan 1;2019:bay141. doi: 10.1093/database/bay141.
Enhancers can act as cis-regulatory elements to control transcriptional regulation by recruiting DNA-binding transcription factors (TFs) in a tissue-specific manner. Recent studies show that enhancers regulate not only protein-coding genes but also microRNAs (miRNAs), and mutations within the TF binding sites (TFBSs) located on enhancers will cause a variety of diseases such as cancer. However, a comprehensive resource to integrate these regulation elements for revealing transcriptional regulations in the context of enhancers is not currently available. Here, we introduce EnhancerDB, a web-accessible database to provide a resource to browse and search regulatory relationships identified in this study, including 131 054 581 TF-enhancer, 17 059 enhancer-miRNAs, 318 993 enhancer-genes, 4 639 558 TF-miRNAs, 1 059 695 TF-genes, 11 439 394 enhancer-single-nucleotide polymorphisms (SNPs) and 23 334 genes associated with expression quantitative trait loci (eQTL) SNP and expression profile of TF/gene/miRNA across multiple human tissues/cell lines. We also developed a tool that further allows users to define tissue-specific enhancers by setting the threshold score of tissue specificity of enhancers. In addition, links to external resources are also available at EnhancerDB.
增强子可以作为顺式调控元件，通过组织特异性地招募 DNA 结合转录因子 (TFs) 来控制转录调控。最近的研究表明，增强子不仅可以调节蛋白质编码基因，还可以调节 microRNAs (miRNAs)，位于增强子上的 TF 结合位点 (TFBSs) 内的突变会导致多种疾病，如癌症。然而，目前还没有一个综合的资源来整合这些调节元件，以揭示增强子背景下的转录调控。在这里，我们介绍 EnhancerDB，这是一个可访问的网络数据库，提供了一个资源，用于浏览和搜索在本研究中识别出的调控关系，包括 131054581 个 TF-增强子、17059 个增强子-miRNAs、318993 个增强子-基因、4639558 个 TF-miRNAs、1059695 个 TF-基因、11439394 个增强子-单核苷酸多态性 (SNP) 和 23334 个与表达数量性状基因座 (eQTL) SNP 和 TF/基因/miRNA 表达谱相关的基因，这些基因在多种人类组织/细胞系中都有表达。我们还开发了一个工具，允许用户通过设置增强子组织特异性的阈值分数来定义组织特异性增强子。此外，EnhancerDB 还提供了到外部资源的链接。
