261e5208364f3825a86f8a80256e841a7b8f7507 jnavarr5 Fri Nov 22 15:46:11 2019 -0800 Editing the track description page to have line lengths less than 100 characters and indenting the HTML list, refs #23888 diff --git src/hg/makeDb/trackDb/epdNewPromoter.html src/hg/makeDb/trackDb/epdNewPromoter.html index 61b729a..73db55e 100644 --- src/hg/makeDb/trackDb/epdNewPromoter.html +++ src/hg/makeDb/trackDb/epdNewPromoter.html @@ -1,85 +1,81 @@ <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 +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> +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> -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. +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.</p> <p> For 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>. 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>