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    1.Database content and construction

    2.Overall workflow and a self-determined method

    3.How to use the ENdb?

    4.Explanation of the definitions used by the website

    5.Development environment

1.Database content and construction.

Database content and construction.The user-friendly interface was provided to search,browse,download and visualize the detailed information.

2.Overall workflow and a self-determined method


3.How to use the ENdb?

The ‘Data-Browse’ page is organized as an interactive and alphanumerically sortable table that allows users to quickly search for samples and customize filters through ‘Species’, ‘Biosample name’, ‘Enhancer experiment’, and ‘Disease’. The ‘Show entries’ drop-down menu are provided for changing the number of records per page conveniently. Viewing the detailed enhancer information, users can simply search the ‘Enhancer ID’.




In order to help users to view the proximity information of enhancers in the genome intuitively, we developed a personalized genome browser using JBrowse and added a lot of useful tracks. Users see the proximity of enhancers to nearby genes, genome segments, SNPs and TFs.



If you want to share your data, please fill out the necessary information in the form below and we will add it to ENdb soon. Thank you.



The data of Enhancers and their elements of all samples are provided for download in the ‘Download’ page. Users can download their files of interest.


4.Explanation of the definitions used by the website
ENdb database contains 22 columns separated by tab:Description
ENdb database contains 22 columns separated by tab:Description
Biosample_name The specific tissues or cells use in the experiment.
Experiment_class The experimental categories (Low+high-throughput or Low-throughput).
Enhancer_experiment The experiments used to confirm the activity of enhancer.
Enhancer_experiment_description The experimental description of the enhancer.
Enhancer_type Enhancer or Super-enhancer.
Target_gene The target gene of enhancer is confirmed by experiments.
Strong_evidence e.g., CRISPR/Cas9,3C,q3C,3C-qPCR,ChIP-3C,3C-qPCR,3C-seq,4C,4C-seq,5C.
Less_strong_evidence e.g., ChIP-seq,Western blot,Luciferase Reporter Assay.
Target_gene_experiment_description The details on experimental enhancer.
Target_gene_aliases The aliases of target gene.
Disease The disease name.
Enhancer_function The function of enhancers is verified experimentally.
Enhancer_function_experimen The experiments on the function.
Enhancer_function_experiment_description The in-text experimental description of the function.
TF_name The name of the transcription factor.
TF_aliases The aliases of gene.
TF_Experiment The experiments on the TF.
TF_experiment_description The experimental description of TF.
SNP_ID The definition SNP of GWAS.
SNP_position The position of SNP.
SNP_experiment The experiments on the SNP in the region of enhancers.
Distance_from_TSS The distance of the enhancer and the target gene.
5.Development environment
Development environment

The current version of ENdb is developed using MySQL 5.7.17 (http://www.mysql.com) and runs on a Linux-based Apache Web server (http://www.apache.org). The server-side scripting is PHP 7.0 (http://www.php.net) . We designed and built the interactive interface using Bootstrap v3.3.7 (https://v3.bootcss.com) and JQuery v2.1.1 (http://jquery. com). We used ECharts (http://echarts.baidu.com) and D3 (https://d3js.org) as a graphical visualization framework, and JBrowse (http://jbrowse.org) is the genome browser framework. We recommend using a modern web browser that supports the HTML5 standard such as Firefox, Google Chrome, Safari, Opera or IE 9.0+ for the best display.

The ENdb database is freely available to the research community using the web link (http://www.licpathway.net/ENdb). Users are not required to register or login to access features in the database.

Material disclaimer

The materials and frameworks used by ENdb are shared by the network and do not contain intellectual property infringement. If there is any infringement, please write to us and we will change it in time.

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