ENdb: a manually curated database of experimentally supported enhancers for human and mouse

Abstract

Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons. Enhancers, as well as their associated target genes, and transcription factors (TFs) that bind to them, are highly associated with human disease and biological processes. Although some enhancer databases have been published, most only focus on enhancers identified by high-throughput experimental techniques. Therefore, it is highly desirable to construct a comprehensive resource of manually curated enhancers and their related information based on low-throughput experimental evidences. Here, we established a comprehensive manually-curated enhancer database for human and mouse, which provides a resource for experimentally supported enhancers, and to annotate the detailed information of enhancers. The current release of ENdb documents 737 experimentally validated enhancers and their related information, including 384 target genes, 263 TFs, 110 diseases and 153 functions in human and mouse. Moreover, the enhancer-related information was supported by experimental evidences, such as RNAi, in vitro knockdown, western blotting, qRT-PCR, luciferase reporter assay, chromatin conformation capture (3C) and chromosome conformation capture-on-chip (4C) assays. ENdb provides a user-friendly interface to query, browse and visualize the detailed information of enhancers. The database is available at http://www.licpathway.net/ENdb.

VARAdb: a comprehensive variation annotation database for human

“…To provide a comprehensive enhancer resource for variation annotation, the current release of VARAdb collected four major types of enhancers. They consist of 1 535 disease enhancers from DiseaseEnhancer ( 55 ) and EnDisease 2.0 ( 56 ), 1 416 experimentally validated enhancers from VISTA Enhancer Browser ( 57 ) and ENdb ( 58 ), 877 955 active enhancers from HACER GRO-seq/PRO-seq enhancers ( 59 ) and the FANTOM5 project ( 60 ), and 6 629 274 typical enhancers from SEdb that included 542 human H3K27ac samples from >240 tissues and cell types ( 50 ).…”

Characterization of super‐enhancer‐associated functional lncRNAs acting as ceRNAs in ESCC

“…Because SEs are frequently identified near protein-coding genes (PCGs) or noncoding RNAs that are important for controlling cell identity and differentiation, characterizing the function of SEs provides an opportunity to quickly identify key nodes driving diseases and biological processes (Hnisz et al, 2013(Hnisz et al, , 2015Jiang et al, 2019;Qian et al, 2019;Tang et al, 2019). Recently, some enhancer databases were developed, including SEdb (Jiang et al, 2019), db-SUPER (Khan and Zhang, 2016), SEA (Wei et al, 2016), and ENdb (Bai et al, 2020). These databases provided a large number of SE/TE regions and related annotation information for various tissue/cell types.…”

Integrative Epigenomic Analysis of Transcriptional Regulation of Human CircRNAs

“…Super-enhancers (SEs) play key regulatory roles in transcriptional activation in both normal cell development and disease states (Hnisz et al, 2013 ; Loven et al, 2013 ; Jiang et al, 2019 ; Qian et al, 2019 ; Bai et al, 2020 ). Very recently, Bin et al identified an SE-regulated circRNAs (circNfix), which has important functions in cardiomyocyte proliferation and angiogenesis (Huang et al, 2019 ).…”