Context-Specific Epigenetic Regulatory Network Database for Alzheimer’s Disease
Database Website: https://bioed.bu.edu/students_24/Team_10/Team-10_database.html
Project Overview Video: Available on the homepage of the live site.
⚠️ Note: This repository contains the source code used for the Boston University deployment. Some asset paths are configured for the BU course server environment.
cEpiReg constructs a comprehensive database elucidating the intricate regulatory mechanisms underlying Alzheimer's Disease (AD) genetics.
By integrating:
- Single-cell RNA-seq (scRNA-seq)
- Single-cell ATAC-seq (scATAC-seq)
- eQTL analysis
- Public databases (ENCODE, Epimap, GWAS Catalog, UCSC, dbSNP)
we identified and connected:
- Transcription Factors (TFs)
- Target Genes (TGs)
- Cis-Regulatory Elements (CREs)
- Disease-associated SNPs
This project establishes a regulatory framework linking TF → CRE → Target Gene → Genetic Variant, uncovering hidden regulatory relationships critical for understanding AD pathogenesis.
Done in collaboration with the Hou Lab.
The cEpiReg framework integrates multiple analytical pipelines:
- Built GRNs using pySCENIC
- Identified transcription factor → target gene relationships
- Linked cis-regulatory elements to genes
- Cross-referenced with ENCODE and Epimap datasets
- Associated SNPs with genes and CREs
- Connected regulatory variation to disease genetics
- Interactive query interface
- Downloadable data tables (.csv, .txt)
- External database linking (UCSC, dbSNP)
- Network visualizations (NetworkX + Plotly)
- Integrated help documentation
While full multi-layer integration was limited by cell-type and tissue-specific sample constraints, the platform successfully integrates independent regulatory modules into a cohesive database interface.
- Gene and region query functionality
- Interactive network visualizations
- Downloadable query results (.csv / .txt)
- External database integration (UCSC Genome Browser, dbSNP)
- Heatmaps and CRE visualizations
- Structured navigation across GRN, CRE Explorer, and eQTL modules
- Comprehensive help page
| File | Description |
|---|---|
Team-10_database.html |
Homepage |
GRN-test.html / grn-test.py |
Gene Regulatory Network module |
ATAC.html / ATAC_AJAX.py |
CRE Explorer module |
eQTL-data.html / eqtl.py |
CRE + eQTL integration module |
styles.css / style1.css |
Website styling |
Database_Overview.mp4 |
Demo video |
NR-biorender-cepireg-logo.png |
Project logo |
- Designed homepage, navigation UI, and Help page
- Developed GRN query system and visualizations
- Implemented interactive networks using NetworkX + Plotly
- Enabled downloadable visualizations (.png) and tables (.csv)
- Designed CRE Explorer module
- Implemented Pie Charts, Data Tables, and IGV integration
- Enabled .txt download functionality
- Contributed to Help page revisions
- Designed CRE + eQTL module
- Integrated UCSC/dbSNP external links
- Implemented Google Charts heatmap visualization
- Enabled downloadable .csv outputs
- Help page design contributions
Fu, T. T., Mahendran, J., Kapalli, B., Rao, N., Farrer, L., & Hou, L. (2025). W50. Epigenetic regulatory network in microglia reveals context-dependent trans-regulatory programs in brain disease. European Neuropsychopharmacology, 99, 234.
Fu, T. T., Kapalli, B., Mahendran, J., Rao, N., & Hou, L. (2024). Leveraging context-specific epigenomic regulatory networks (EPINETS) to dissect the genetics of neuropsychiatric disorders. European Neuropsychopharmacology, 87, 8.
We extend our heartfelt gratitude to:
- Dr. Lei Hou
- Dr. Ting-Ting Fu
for their mentorship, guidance, and expertise throughout the development of the cEpiReg-Database.
The database was developed at Boston University as part of the BF768 course (Spring 2024).
- Python
- pySCENIC
- NetworkX
- Plotly (JavaScript)
- Google Charts
- HTML / CSS
- AJAX
- UCSC Genome Browser integration