Division of Biostatistics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America.
Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America.
PLoS One. 2020 Dec 15;15(12):e0243791. doi: 10.1371/journal.pone.0243791. eCollection 2020.
Enhancers are powerful and versatile agents of cell-type specific gene regulation, which are thought to play key roles in human disease. Enhancers are short DNA elements that function primarily as clusters of transcription factor binding sites that are spatially coordinated to regulate expression of one or more specific target genes. These regulatory connections between enhancers and target genes can therefore be characterized as enhancer-gene links that can affect development, disease, and homeostatic cellular processes. Despite their implication in disease and the establishment of cell identity during development, most enhancer-gene links remain unknown. Here we introduce a new, publicly accessible database of predicted enhancer-gene links, PEREGRINE. The PEREGRINE human enhancer-gene links interactive web interface incorporates publicly available experimental data from ChIA-PET, eQTL, and Hi-C assays across 78 cell and tissue types to link 449,627 enhancers to 17,643 protein-coding genes. These enhancer-gene links are made available through the new Enhancer module of the PANTHER database and website where the user may easily access the evidence for each enhancer-gene link, as well as query by target gene and enhancer location.
增强子是细胞类型特异性基因调控的强大而多功能的因子，被认为在人类疾病中发挥关键作用。增强子是短的 DNA 元件，主要作为转录因子结合位点的簇发挥作用，这些位点在空间上协调以调节一个或多个特定靶基因的表达。因此，增强子和靶基因之间的这些调节连接可以被描述为增强子-基因连接，这些连接可以影响发育、疾病和细胞内稳态过程。尽管它们与疾病有关，并且在发育过程中建立了细胞身份，但大多数增强子-基因连接仍然未知。在这里，我们介绍了一个新的、可公开访问的预测增强子-基因连接数据库，PEREGRINE。PEREGRINE 人类增强子-基因连接交互式网络界面整合了来自 ChIA-PET、eQTL 和 Hi-C 测定的 78 种细胞和组织类型的公开可用的实验数据，将 449,627 个增强子与 17,643 个蛋白质编码基因连接起来。这些增强子-基因连接可通过 PANTHER 数据库和网站的新增强子模块获得，用户可以轻松访问每个增强子-基因连接的证据，也可以根据靶基因和增强子位置进行查询。
