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Updated: Jul 17, 2026
08:12
A Web-Based Workflow for Selecting Gene- and Tissue-Specific Enhancers
Published on: July 18, 2025
EnhancerDB 2.0: a comprehensive cross-species enhancer atlas
Junnuo Zheng1, Yukun Li1, Xingyi Du1
1School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu China.
Molecular Biology and Evolution
|July 15, 2026
Summary
EnhancerDB 2.0 is a powerful database for studying enhancers, which regulate gene expression. This updated resource expands to five species and offers extensive multi-omics data for biological and medical research.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Enhancers are crucial cis-regulatory elements controlling gene expression during development and adaptation.
- Large-scale omics data necessitates advanced tools for analyzing enhancer regulatory networks.
- Existing resources may lack multi-species coverage and comprehensive annotation.
Purpose of the Study:
- To update and expand EnhancerDB 1.0 into EnhancerDB 2.0 for enhanced profiling of enhancer regulatory networks.
- To facilitate multi-omics interpretation of gene regulation by enhancers.
- To provide a comprehensive, user-friendly platform for enhancer research.
Main Methods:
- Expanded EnhancerDB 2.0 to include five species: human, mouse, zebrafish, fruit fly, and yeast.
- Integrated extensive annotations including transcription factor binding sites, target genes/miRNAs/lncRNAs, SNPs, CRISPR-Cas9 sites, chromatin accessibility, repeat regions, methylation sites, and GWAS entries.
- Developed an improved search function and a new analysis module for generating publication-quality charts.
Main Results:
- EnhancerDB 2.0 now contains 1,605,856 enhancer entries across five species.
- Nearly 100 million annotated entries provide rich functional and regulatory information.
- The platform offers enhanced search capabilities and data visualization tools.
Conclusions:
- EnhancerDB 2.0 is a significantly expanded and enriched resource for studying enhancer function and regulation.
- It serves as a valuable, user-friendly platform for researchers in biology, medicine, and genetics.
- The database supports comprehensive analysis of enhancer-mediated gene regulation across multiple species.
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