Enhancers are distal cis-regulatory DNA elements that positively regulate the transcription of target genes in a tissue-specific and spatiotemporal-specific manner. To elucidate the contextual functions and regulatory networks of cis-regulatory elements, we previously developed EnhancerDB 1.0, which has been widely used in gene regulation research. With the rapid growth of large-scale omics data in recent years, there is an increasing need to update and expand existing databases to support emerging research demands. Therefore, we have developed EnhancerDB 2.0 (https://lcbb.swjtu.edu.cn/enhancerDB2.0/), an updated online resource designed to provide comprehensive enhancer-regulated networks. EnhancerDB 2.0 significantly enhances its predecessor by incorporating data from five species (human, mouse, zebrafish, fruit fly, and yeast), increasing the number of enhancer entries, and integrating extensive annotations such as lncRNAs, methylation sites, repeat elements, chromatin accessibility, CRISPR-Cas9 sites, and FASTA format sequences. Additionally, it features improved search functionalities and a new analysis module capable of generating publication-quality figures. In summary, EnhancerDB 2.0 is a comprehensive update of EnhancerDB 1.0, featuring more enhancers and enriched annotation information. It provides a user-friendly platform for researchers to better explore the regulatory roles of enhancer.
Allow users to click on the left side to select different species (Human/Mouse/Zebrafish/Fly/Yeast), different sample types, different tissues/cell lines sources of sample to browse, the right side will display EnhancerID, Species, Location, Size, Tissue/Cell line, Disease/Health, Tissues harboring the enhancer, Data Source clicking on the EnhancerID will display detailed information about the enhancer, including Enhancer Details and Enhancer annotation. If you click on the annotation inforrmation of font text, it will show the details information of the element.
URL:https://lcbb.swjtu.edu.cn/enhancerDB2.0/html/browse.php
Here are the results of the detail information of enh116291.
URL:https://lcbb.swjtu.edu.cn/enhancerDB2.0/html/search.php
Search for enhancer by species and sample source.
Search enhancer by TF.
Search for enhancer regions of interest to the user by customizing intervals.
Search diffenert species enhancer data by SNP.
Search diffenert species enhancer data by miRNA.
Search human enhancer data by eQTL.
Search tissue/cell-specific or ubiquitous enhancers
URL:https://lcbb.swjtu.edu.cn/enhancerDB2.0/html/analysis.php
URL:https://lcbb.swjtu.edu.cn/enhancerDB2.0/html/analysis.php
This module is comparative analysis, where users can select species, then select two samples, and finally generate similarities and differences between the two samples.
The results of the analysis of the example data are as follows.
URL:https://lcbb.swjtu.edu.cn/enhancerDB2.0/html/analysis.php
This module is for gene and enhancer analysis. Users first input multiple human gene names, then submit them, and finally generate detailed information about these genes, as well as enhancer information that regulates these genes.
The results of the analysis of the example data are as follows.
URL:https://lcbb.swjtu.edu.cn/enhancerDB2.0/html/analysis.php
This module is for miRNA and enhancer analysis. Users first input multiple miRNA names, then submit them, and finally generate detailed information about these miRNAs, as well as enhancer information that regulates these miRNAs.
The results of the analysis of the example data are as follows.
URL:https://lcbb.swjtu.edu.cn/enhancerDB2.0/html/analysis.php
This module is for enhancer random analysis. Users first input a bed file of enhancer coordinates, then submit it, and finally generate some enhancer information of similar length to these enhancers.
The results of the analysis of the example data are as follows.
URL:https://lcbb.swjtu.edu.cn/enhancerDB2.0/html/analysis.php
This module is for enhancer overlap analysis. Users first input a bed file of enhancer coordinates, then select the overlap ratio, submit it, and finally generate some enhancer information that overlaps with these enhancers.
The results of the analysis of the example data are as follows.
URL:https://lcbb.swjtu.edu.cn/enhancerDB2.0/html/analysis.php
This module is for analyzing the distribution of enhancer. Users first input a bed file of enhancer coordinates, then submit it, and finally generate publication-quality figure for enhancer chromosomal distribution.
The results of the analysis of the example data are as follows.
URL:https://lcbb.swjtu.edu.cn/enhancerDB2.0/html/analysis.php
This module is for analyzing the GC content of enhancer. Users first input a bed file of enhancer coordinates, then submit it, and finally generate publication-quality GC enrichment figure of enhancer.
The results of the analysis of the example data are as follows.
URL:https://lcbb.swjtu.edu.cn/enhancerDB2.0/html/analysis.php
This module is for analyzing the distribution of enhancers. Users first input a bed file of enhancer coordinates, then submit it, and finally generate publication-quality figure for length distribution and cumulative frequency of enhancer.
The results of the analysis of the example data are as follows.
URL:https://lcbb.swjtu.edu.cn/enhancerDB2.0/html/download.php
The corresponding enhancer information results for each species as well as annotation information can be downloaded from the "Download" page. Users can quickly download the relevant information.
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