- Found free promoters database at the Swiss Institute of Bioinformatics Eukaryotic Promoter Database (EPD) website
- Retrieved BED file of all human promoters from: http://epd.vital-it.ch/get_promoters.php
- Selected H. sapiens, left all other options blank, clicked [select], downloaded BED file, uploaded to Galaxy as Promoters EPD All
- Total promoters: 23,316
- Each is only 10 bp long
- Gene names are included!
- Note: Custom-generated promoter file (500 bp TSS regions) = 26,960. This is over 3k more than the EPD.
New Galaxy files
Note: EPD allows selection of promoter sub-classes
- All EPD promoters - uploaded as Promoters EPD All
- TATA-box motif - Promoters EPD TATA = 2,007 regions
- Initiator motif - Promoters EPD Init = 6,538 regions
- CCAAT-box motif - Promoters EPD CCAAT = 3,838 regions
- GC-box motif - Promoters EPD GC = 10,695 regions
- CpG (unable to retrieve...looks like criteria have not been added yet)