|Coverage:||10728 promoters, 10235 genes|
|Genome assembly:||D. rerio (July 2010 Zv9/danRer7)|
|Gene annotation||UCSC known genes (30-Jun-2013)|
|Based on data from:||
Nepal et al, Genome Res. 2013, [ 24002785 ]
|Documentation files||Promoter assembly pipeline description|
Various tools allow you to analyse promoters from EPD and/or to select subsets of promoters. In order to analyze the complete EPD promoter set, go directly to one of the analysis pages. If you prefer to first select a subset of promoters, go to one of the selection pages. From the output of the selection pages you can then directly navigate to one of the analyses pages, or you can continue with another selection page to refine your promoter selection.
|How-To Documentation: OProf, FindM and ChIP-Cor.|
Core promoter element analysis is performed in order to investigate the quality of the promoter collection. It exploits the fact that certain DNA motifs preferentially occur at characteristic distances from a TSS. For instance, the TATA-box occurs in a narrow region centered about 28 bp upstream of the TSS whereas the CCAAT-box occurs in a much wider area with a peak frequency at position −80. Based on these observations, we would expect a high-quality promoter collection to show high peaks for both sequence motifs. In addition, a narrow TATA-box peak at −28 would indicate precise TSS mapping. This analysis has been performed using OProf. Readers are encouraged to repeat this anlysis and perform others in order to check for the quality of the promoter list.
TATA-box: this core promoter element is normally found 28 bp upstream the transcription start site. The following plot shows that EPDnew promoter collection has a more focused TATA-box distribution compared to ENSEMBL annotation suggesting a precise TSS mapping in EPDnew.
Initiator: it is found at the TSS and shows a great enrichemnt in EPDnew compared to ENSEMBL promoter collection.
CCAAT-box: is found more up-stream of the TSS compared to the other core promoter elements. EPDnew shows an erichment in this elemnts as well.
GC-box: as in the other cases, EPDnew shows an enrichemnt in this lemnt comapered to ENSEMBL collection.