EPDnew selection tool

Use this tool to select all promoters (leaving all 'Optional criterias' blank) or restrict them based on all or some of their genomic contexes (such as presence of core promoter elements) or expression levels. After selection, you can download them in various format (for example in FASTA, BED, etc...), liftOver them to a different assembly or use them to perform further analysis such as motif enrichment/search and chromatin status.

Select promoters for
Optional criteria:
TATA-box motif
Initiator motif
CCAAT motif
GC motif
CpG island
marked as
average expression of at least tags
expressed in at least samples



Rules used in selection

TATA-box: a promoter is with a TATA-box if the motif is found at position −28 (± 3 bp) from the transcription start site (evaluated using FindM).
Initiator: a promoter is with an Initiator motif if it is found at position 0 from the transcription start site (evaluated using FindM).
CCAAT-box: a promoter is with a CCAAT motif if it is found in the region −200 to −50 from the transcription start site (evaluated using FindM).
GC-box: a promoter is with a GC motif if it is found in the region −200 to −50 from the transcription start site (evaluated using FindM).
CpG: at the moment this selection criteria is not active.
Average Expression: for each sample used in generating EPDnew collection, the promoter expression is calculated as the number of CAGE tags matching the region from −250 to +250 bp from the TSS. Each sample is normalized to a total tag count of 10M.
Expression call: a promoter is expressed in sample X if the number of tags that map at the TSS is higher than 3.
Last update Dec. 2016