The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
Nucleic Acids Res. 2024 Jan 5;52(D1):D81-D91. doi: 10.1093/nar/gkad925.
Enhancer RNAs (eRNAs) transcribed from distal active enhancers serve as key regulators in gene transcriptional regulation. The accumulation of eRNAs from multiple sequencing assays has led to an urgent need to comprehensively collect and process these data to illustrate the regulatory landscape of eRNAs. To address this need, we developed the eRNAbase (http://bio.liclab.net/eRNAbase/index.php) to store the massive available resources of human and mouse eRNAs and provide comprehensive annotation and analyses for eRNAs. The current version of eRNAbase cataloged 10 399 928 eRNAs from 1012 samples, including 858 human samples and 154 mouse samples. These eRNAs were first identified and uniformly processed from 14 eRNA-related experiment types manually collected from GEO/SRA and ENCODE. Importantly, the eRNAbase provides detailed and abundant (epi)genetic annotations in eRNA regions, such as super enhancers, enhancers, common single nucleotide polymorphisms, expression quantitative trait loci, transcription factor binding sites, CRISPR/Cas9 target sites, DNase I hypersensitivity sites, chromatin accessibility regions, methylation sites, chromatin interactions regions, topologically associating domains and RNA spatial interactions. Furthermore, the eRNAbase provides users with three novel analyses including eRNA-mediated pathway regulatory analysis, eRNA-based variation interpretation analysis and eRNA-mediated TF-target gene analysis. Hence, eRNAbase is a powerful platform to query, browse and visualize regulatory cues associated with eRNAs.
增强子 RNA（eRNA）由远端活性增强子转录而来，是基因转录调控的关键调节剂。多个测序分析中 eRNA 的积累，使得我们迫切需要全面收集和处理这些数据，以阐明 eRNA 的调控图谱。为了满足这一需求，我们开发了 eRNAbase（http://bio.liclab.net/eRNAbase/index.php），用于存储大量的人类和小鼠 eRNA 可用资源，并为 eRNA 提供全面的注释和分析。目前的 eRNAbase 版本收录了 1012 个样本中 10399928 个 eRNA，包括 858 个人类样本和 154 个小鼠样本。这些 eRNA 首先从 GEO/SRA 和 ENCODE 中手动收集的 14 种 eRNA 相关实验类型中进行鉴定和统一处理。重要的是，eRNAbase 在 eRNA 区域提供了详细和丰富的（表观）遗传注释，例如超级增强子、增强子、常见单核苷酸多态性、表达数量性状位点、转录因子结合位点、CRISPR/Cas9 靶位点、DNase I 超敏位点、染色质可及性区域、甲基化位点、染色质相互作用区域、拓扑关联域和 RNA 空间相互作用。此外，eRNAbase 还为用户提供了三种新的分析，包括 eRNA 介导的通路调控分析、eRNA 变异解释分析和 eRNA 介导的 TF-靶基因分析。因此，eRNAbase 是一个强大的平台，用于查询、浏览和可视化与 eRNA 相关的调控线索。
