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Peer-reviewedCC BY 4.0Nucleic Acids Research

ENdb 2.0: an updated database of experimentally supported enhancers

  • Mingcong Xu1,2
  • Guorui Zhang1
  • Qiuyu Wang1
  • Yiqing Chen3
  • Chao Song1
  • Jiaqi Liu1
  • Bingzhou Guo4
  • Jia Zhou1,5
  • Chunquan Li1,3,6,7
7 affiliations
  1. 1The 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 ,
  2. 2School of Computer Science and Technology, Harbin University of Science and Technology , Harbin 150080 ,
  3. 3School of Traditional Chinese Medicine, Beijing University of Chinese Medicine , Beijing 100029 ,
  4. 4School of Computer Science and Technology, Shandong University , Qingdao 266237 ,
  5. 5Department of Ultrasound Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China , Hengyang 421002 ,
  6. 6National Health Commission Key Laboratory of Birth Defect Research and Prevention & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China , Hengyang, Hunan 421001 ,
  7. 7NHC Key Laboratory of Neurodegenerative diseases, University of South China Hengyang, Hunan 421001 ,
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Abstract

Enhancers are cis-regulatory elements that control gene expression during development, cell differentiation, and disease. Genome-wide studies have mapped large numbers of candidate regulatory elements, but experimentally supported enhancer information remains dispersed across primary studies and experimental systems. Here, we present ENdb 2.0 (http://www.licpathway.net/ENdb/index.php), an updated, manually curated database of experimentally supported enhancers. Compared with ENdb 1.0, the major updates are (i) literature coverage through 2026 and five species: Homo sapiens, Mus musculus, Drosophila melanogaster, Danio rerio, and Rattus norvegicus; (ii) 4831 enhancer evidence records, including 2793 enhancer–TF–target-gene records involving 496 TFs and 1070 target genes; (iii) expanded curation of genomic coordinates, experimental evidence, enhancer type, regulatory state, biological condition, tissues, cell sources, cell types, and diseases, covering 169 tissues, 1255 cell sources, 415 cell types, and 226 diseases; and (iv) biological search, genome browsing, pathway enrichment analysis, agent-assisted query, and structured data download. ENdb 2.0 links experimentally supported enhancer regions with regulatory factors, target genes, biological conditions, and supporting experiments across physiological and disease states.

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Cite

BibTeXRIS
BibTeX
@article{xu2026endb,
  title = {{ENdb 2.0: an updated database of experimentally supported enhancers}},
  author = {Mingcong Xu and Guorui Zhang and Qiuyu Wang and Yiqing Chen and Chao Song and Jiaqi Liu and Bingzhou Guo and Jia Zhou and Chunquan Li},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag1074},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1074/9005082},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - ENdb 2.0: an updated database of experimentally supported enhancers
AU  - Mingcong Xu
AU  - Guorui Zhang
AU  - Qiuyu Wang
AU  - Yiqing Chen
AU  - Chao Song
AU  - Jiaqi Liu
AU  - Bingzhou Guo
AU  - Jia Zhou
AU  - Chunquan Li
PY  - 2026
DA  - 2026/10/30
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1074
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1074/9005082
AB  - Enhancers are cis-regulatory elements that control gene expression during development, cell differentiation, and disease. Genome-wide studies have mapped large numbers of candidate regulatory elements, but experimentally supported enhancer information remains dispersed across primary studies and experimental systems. Here, we present ENdb 2.0 (http://www.licpathway.net/ENdb/index.php), an updated, manually curated database of experimentally supported enhancers. Compared with ENdb 1.0, the major updates are (i) literature coverage through 2026 and five species: Homo sapiens, Mus musculus, Drosophila melanogaster, Danio rerio, and Rattus norvegicus; (ii) 4831 enhancer evidence records, including 2793 enhancer–TF–target-gene records involving 496 TFs and 1070 target genes; (iii) expanded curation of genomic coordinates, experimental evidence, enhancer type, regulatory state, biological condition, tissues, cell sources, cell types, and diseases, covering 169 tissues, 1255 cell sources, 415 cell types, and 226 diseases; and (iv) biological search, genome browsing, pathway enrichment analysis, agent-assisted query, and structured data download. ENdb 2.0 links experimentally supported enhancer regions with regulatory factors, target genes, biological conditions, and supporting experiments across physiological and disease states.
SN  - 0305-1048
SN  - 1362-4962
ER  -