EPDnew Promoters Track Settings
 
Promoters from EPDnew   (All Expression and Regulation tracks)

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 EPDnew v6  Promoters from EPDnew mouse version 003   Schema 
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new Note: Track Released Nov. 27, 2019

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.