Our database provides comprehensive datasets of enhancer perturbation experiments, including raw data, processed results, and supplementary materials. All datasets are available in standard formats (xlsx, bed, csv, tsv) and are regularly updated.
| Dataset | Description | Format | Size | Last Updated | Action |
|---|---|---|---|---|---|
| Complete Database | Full database dump including all enhancer perturbation experiments | xlsx | 13MB | 2024-02-20 | Download |
| Enhancer Coordinates | Genomic coordinates of all enhancers | xlsx | 156 MB | 2024-02-20 | Download |
| Enhancer Activity Data | Interactive visualization of enhancer activity across tissues | HTML/JS | 2.1 MB | 2024-02-20 | View |
| Enhancer - TF activity data | Data on enhancer and transcription factor activity relationships. | Directory | N/A | 2025-09-23 | View |
| Enhancer-gene-list | Enhancer gene relationships and annotations | bed | 45 MB | 2024-02-20 | Download |
| Pathway Enrichment Script | Stand-alone Python script for enhancer pathway enrichment analysis | py | 17 KB | 2025-05-13 | Download |
| Enhancer Simple info (UCSC bed detail file) | Simplified enhancer details in BED format | bed | 15 MB | 2024-02-20 | |
| Enhancer Details (UCSC bed detail file) | Comprehensive enhancer details in BED format | bed | 31 MB | 2024-02-20 | Download |
| Database TSV | Complete database in tab-separated format | tsv | 48 MB | 2024-02-20 | Download |
| Database CSV | Complete database in comma-separated format | csv | 48 MB | 2024-02-20 | Download |
The pathway enrichment Python script allows you to perform enhancer pathway enrichment analysis locally on your own machine. This is the same script that powers our web-based analysis tool.
python pathway_enrichment.py --bed your_input.bed --enhancer enhancer_gene.bed --gmt_dir gmt_directory
For more detailed usage instructions and additional options, download the script and run:
python pathway_enrichment.py --help
Total Publications: 35
Publications added to database: Download CSV
| Paper_title | doi |
|---|---|
| CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription | https://doi.org/10.1101/2024.10.08.616922 |
| High-resolution interrogation of functional elements in the noncoding genome | https://doi.org/10.1126/science.aaf7613 |
| CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression | https://doi.org/10.1158/0008-5472.can-23-3995 |
| Genome-wide Cas9-mediated screening of essential non-coding regulatory elements via libraries of paired single-guide RNAs | https://doi.org/10.1038/s41551-024-01204-8 |
| CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant | https://doi.org/10.1016/j.celrep.2024.114640 |
| A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer | https://doi.org/10.1038/s41467-022-31919-8 |
| STAT3-Mediated Promoter-Enhancer Interaction Up-Regulates Inhibitor of DNA Binding 1 (ID1) to Promote Colon Cancer Progression | https://doi.org/10.3390/ijms241210041 |
| Enhancer RNA Transcription Is Essential for a Novel CSF1 Enhancer in Triple-Negative Breast Cancer | https://doi.org/10.3390/cancers14071852 |
| Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath | https://doi.org/10.1126/sciadv.abi4360 |
| Androgen Receptor-Activated Enhancers Simultaneously Regulate Oncogene TMPRSS2 and lncRNA PRCAT38 in Prostate Cancer | https://doi.org/10.3390/cells8080864 |
| Intronic enhancers of the human SNCA gene predominantly regulate its expression in brain in vivo | https://doi.org/10.1126/sciadv.abq6324 |
| Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescenc | https://doi.org/10.1186/s13059-018-1494-1 |
| Massively parallel disruption of enhancers active in human neural stem cells | https://doi.org/10.1016/j.celrep.2024.113693 |
| Deciphering essential cistromes using genome-wide CRISPR screens | https://doi.org/10.1073/pnas.1908155116 |
| TALEN-mediated enhancer knockout influences TNFAIP3 gene expression and mimics a molecular phenotype associated with systemic lupus erythematosus | https://doi.org/10.1038/gene.2016.4 |
| Dynamic-network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer-gene regulatory activity during cell state transitions | //doi.org/10.1038/s41588-023-01450-7 |
| Landscape of enhancer disruption and functional screen in melanoma cells | https://doi.org/10.1186/s13059-023-03087-5 |
| Systematic mapping of functional enhancer-promoter connections with CRISPR interference | https://doi.org/10.1126/science.aag2445 |
| Downregulation of enhancer RNA AC003092.1 is associated with poor prognosis in kidney renal clear cell carcinoma | https://doi.org/10.1038/s41598-024-64431-8 |
| eNEMAL, an enhancer RNA transcribed from a distal MALAT1 enhancer, promotes NEAT1 long isoform expression | https://doi.org/10.1371/journal.pone.0251515 |
| Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation | https://doi.org/10.1038/nature12210 |
| Enhancer RNA - P2RY2e induced by estrogen promotes malignant behaviors of bladder cancer | https://doi.org/10.7150/ijbs.27151 |
| Super-enhancer-associated long noncoding RNA AC005592.2 promotes tumor progression by regulating OLFM4 in colorectal cancer | https://doi.org/10.1186/s12885-021-07900-x |
| Enhancer RNA-driven looping enhances the transcription of the long noncoding RNA DHRS4-AS1, a controller of the DHRS4 gene cluster | https://doi.org/10.1038/srep20961 |
| The super-enhancer-driven lncRNA LINC00880 acts as a scaffold between CDK1 and PRDX1 to sustain the malignance of lung adenocarcinoma | https://doi.org/10.1038/s41419-023-06047-w |
| Super-enhancer-driven lncRNA LIMD1-AS1 activated by CDK7 promotes glioma progression | https://doi.org/10.1038/s41419-023-05892-z |
| Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression | https://doi.org/10.1038/s41467-018-06081-9 |
| Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA | https://doi.org/10.1038/ncomms7520 |
| JUN-induced super-enhancer RNA forms R-loop to promote nasopharyngeal carcinoma metastasis | https://doi.org/10.1038/s41419-023-05985-9 |
| The enhancer RNA ARIEL activates the oncogenic transcriptional program in T-cell acute lymphoblastic leukemia | https://doi.org/10.1182/blood.2018874503 |
| Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis | https://doi.org/10.1158/0008-5472.CAN-23-0544 |
| Carcinogen-induced super-enhancer RNA promotes nasopharyngeal carcinoma metastasis through NPM1/c-Myc/NDRG1 axis | https://pmc.ncbi.nlm.nih.gov/articles/PMC10492133/ |
| RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation | https://doi.org/10.1038/s41594-018-0102-0 |
| Complementary Alu sequences mediate enhancer?promoter selectivity | https://doi.org/10.1038/s41586-023-06323-x |
| The long noncoding RNA SNHG1 regulates colorectal cancer cell growth through interactions with EZH2 and miR-154-5p | https://doi.org/10.1186/s12943-018-0894-x |
If you use our datasets in your research, please cite:
[Citation details will be added upon publication]