849a921db0a5f5e89040171e9da31fc63d2aef0d kate Tue Nov 5 17:28:14 2019 -0800 Minor edit. refs #23888 diff --git src/hg/makeDb/trackDb/epdNewPromoter.html src/hg/makeDb/trackDb/epdNewPromoter.html index 0cc87ee..9fce6fd 100644 --- src/hg/makeDb/trackDb/epdNewPromoter.html +++ src/hg/makeDb/trackDb/epdNewPromoter.html @@ -1,80 +1,80 @@ <h2>Description</h2> <p> These tracks represent the experimentally validated promoters generated by the <a href="https://epd.epfl.ch/" target="_blank">Eukaryotic Promoter Database</a>. </p> <h2>Display Conventions and Configuration</h2> <p> 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. </p> <p> Note that the EPD team has created a <a href="hgHubConnect">public track hub</a> containing promoter and supporting annotations for human, mouse, and other vertebrate and model organism genomes. </p> <h2>Methods</h2> <p> For a description of the methodology and principles used by EPD to predict TSSs, refer to Dreos <i>et al</i>. (2013) in the References section below. A more detailed description of how this data was generated can be found at the following links: <ul> <li> Human promoter pipelines: <a target="_blank" href="https://epd.epfl.ch/epdnew/documents/Hs_epdnew_006_pipeline.php">coding</a>, <a target="_blank" href="https://epd.epfl.ch/epdnew/documents/HsNC_epdnew_001_pipeline.php">non-coding</a> </li> <li> Mouse promoter pipelines: <a target="_blank" href="https://epd.epfl.ch/epdnew/documents/Mm_epdnew_003_pipeline.php">coding</a>, <a target="_blank" href="https://epd.epfl.ch/epdnew/documents/MmNC_epdnew_001_pipeline.php">non-coding</a> </li> </ul> </p> <h2>Credits</h2> <p> Data was generated by the EPD team at the -<a target="_blank" href="https://www.sib.swiss/">Swiss Institute of Bioinformatics</a> +<a target="_blank" href="https://www.sib.swiss/">Swiss Institute of Bioinformatics</a>. For inquiries, contact the EPD team using this <a target="_blank" href="https://epd.epfl.ch/webmail.php">on-line form</a> or email <A HREF="mailto:philipp. bucher@epfl. ch"> philipp. bucher@epfl. ch</A> <!-- above address is philipp.bucher at epfl.ch --> . </p> <h2>References</h2> <p> Dreos R, Ambrosini G, Perier RC, Bucher P. <a href="https://nar.oxfordjournals.org/content/41/D1/D157.full" target="_blank"> EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era</a>. <em>Nucleic Acids Res</em>. 2013 Jan 1;41(D1):D157-64. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23193273" target="_blank">23193273</a>. </p>