EnhancerDB: a resource of transcriptional regulation in the context of enhancers

• DOI: 10.1093/database/bay141
• Publication Date: 2018-12-18T02:42:23Z
• Authors: Ran Kang; Yiming Zhang; Qingqing Huang; Junhua Meng; Ruofan Ding; Yunjian Chang; Lili Xiong; Zhiyun Guo
• Keywords: 0303 health sciences; Mice; MicroRNAs; 03 medical and health sciences; Enhancer Elements, Genetic; Gene Expression Regulation; Databases, Genetic; Animals; Database Management Systems; Humans; Original Article; Software; Transcription Factors

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.