Description
These tracks represent the experimentally validated promoters generated by
the Eukaryotic Promoter Database.
Display Conventions and Configuration
Each item in the track is a representation of the promoter sequence identified by EPD. The
"thin" part of the element represents the 49 bp upstream of the annotated transcription
start site (TSS) whereas the "thick" part represents the TSS plus 10 bp downstream. The
relative position of the thick and thin parts define the orientation of the promoter.
Note that the EPD team has created a public track hub containing
promoter and supporting annotations for human, mouse, and other vertebrate and model organism
genomes.
Methods
Briefly, gene transcript coordinates were obtained from multiple sources (HGNC, GENCODE, Ensembl,
RefSeq) and validated using data from CAGE and RAMPAGE experimental studies obtained from FANTOM 5,
UCSC, and ENCODE. Peak calling, clustering and filtering based on relative expression were applied
to identify the most expressed promoters and those present in the largest number of samples.
For the methodology and principles used by EPD to predict TSSs, refer to Dreos et al.
(2013) in the References section below. A more detailed description of how this data was
generated can be found at the following links:
Credits
Data was generated by the EPD team at the
Swiss Institute of Bioinformatics.
For inquiries, contact the EPD team using this on-line form
or email
philipp.
bucher@epfl.
ch
.
References
Dreos R, Ambrosini G, Perier RC, Bucher P.
EPD and EPDnew, high-quality promoter resources in the
next-generation sequencing era. Nucleic Acids
Res. 2013 Jan 1;41(D1):D157-64. PMID: 23193273.
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