The Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA.
The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
Nucleic Acids Res. 2020 Jan 8;48(D1):D58-D64. doi: 10.1093/nar/gkz980.
Enhancers are distal cis-regulatory elements that activate the transcription of their target genes. They regulate a wide range of important biological functions and processes, including embryogenesis, development, and homeostasis. As more and more large-scale technologies were developed for enhancer identification, a comprehensive database is highly desirable for enhancer annotation based on various genome-wide profiling datasets across different species. Here, we present an updated database EnhancerAtlas 2.0 (http://www.enhanceratlas.org/indexv2.php), covering 586 tissue/cell types that include a large number of normal tissues, cancer cell lines, and cells at different development stages across nine species. Overall, the database contains 13 494 603 enhancers, which were obtained from 16 055 datasets using 12 high-throughput experiment methods (e.g. H3K4me1/H3K27ac, DNase-seq/ATAC-seq, P300, POLR2A, CAGE, ChIA-PET, GRO-seq, STARR-seq and MPRA). The updated version is a huge expansion of the first version, which only contains the enhancers in human cells. In addition, we predicted enhancer-target gene relationships in human, mouse and fly. Finally, the users can search enhancers and enhancer-target gene relationships through five user-friendly, interactive modules. We believe the new annotation of enhancers in EnhancerAtlas 2.0 will facilitate users to perform useful functional analysis of enhancers in various genomes.
增强子是远端顺式调控元件，可激活其靶基因的转录。它们调节广泛的重要生物学功能和过程，包括胚胎发生、发育和体内平衡。随着越来越多的大规模技术被开发用于增强子鉴定，基于不同物种的各种全基因组分析数据集，一个全面的数据库对于增强子注释是非常需要的。在这里，我们展示了一个更新的数据库 EnhancerAtlas 2.0（http://www.enhanceratlas.org/indexv2.php），涵盖了 586 种组织/细胞类型，包括大量正常组织、癌细胞系和来自 9 个物种的不同发育阶段的细胞。总的来说，该数据库包含 13494603 个增强子，这些增强子是从 16055 个数据集使用 12 种高通量实验方法（如 H3K4me1/H3K27ac、DNase-seq/ATAC-seq、P300、POLR2A、CAGE、ChIA-PET、GRO-seq、STARR-seq 和 MPRA）获得的。更新版本是第一个版本的巨大扩展，第一个版本仅包含人类细胞中的增强子。此外，我们预测了人类、小鼠和果蝇中的增强子-靶基因关系。最后，用户可以通过五个用户友好、交互式模块搜索增强子和增强子-靶基因关系。我们相信 EnhancerAtlas 2.0 中增强子的新注释将有助于用户在各种基因组中对增强子进行有用的功能分析。
