Databases
- Disgenet: Metadata for diseases (genes, variants, publications, networks, drugs, etc.):
- Collection of experimental datasets for method validation:
https://docs.google.com/spreadsheets/d/1YQB7GT5zvrCEN00ooQHa-nrpR90Crht3sFHRGgPepf4/edit?usp=sharing
- Link to the folder for group database:
/panfs/pan1.be-md.ncbi.nlm.nih.gov/devdcode/common/database
- A basic readme file for using the mysql database is in the following link:
- New tables
| Table/directory name | Database name | Description | |
|---|---|---|---|
| enhancerActiveWeakMergedPrunedAllTissue | hg19 | all active (no flank) and weak enhancers from Roadmap Project. Neighboring enhancers are merged and longer enhancers (>3kbp) are removed | |
| /net/intdev/devdcode/common/CRISPRi_RNA-seq | GRCh38 | CRISPRi RNA-seq Gene expression data for 77 target TFs plus three controls from the ENCODE project (https://www.encodeproject.org/) | |
| /net/intdev/devdcode/common/ENCODE_phase4/rE2G | GRCh38 | Enhancer gene targets predicted for 323 biosamples based on https://www.biorxiv.org/content/10.1101/2023.11.09.563812v1 | |