00f7911632fbc57aef0298adb49a64e7e7f238ba jnavarr5 Mon Nov 25 15:08:58 2019 -0800 Making line lengths less than 100 characters, refs #23888 diff --git src/hg/makeDb/trackDb/epdNewPromoter.html src/hg/makeDb/trackDb/epdNewPromoter.html index 73db55e..c9701e9 100644 --- src/hg/makeDb/trackDb/epdNewPromoter.html +++ src/hg/makeDb/trackDb/epdNewPromoter.html @@ -1,81 +1,78 @@ <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> +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> +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.</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 +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>