25b689184439ed910a6804062466c7ce30495646 kate Wed Nov 6 15:51:52 2019 -0800 More methods overview -- very brief summary of pipeline docs. refs #23888 diff --git src/hg/makeDb/trackDb/epdNewPromoter.html src/hg/makeDb/trackDb/epdNewPromoter.html index 9fce6fd..61b729a 100644 --- src/hg/makeDb/trackDb/epdNewPromoter.html +++ src/hg/makeDb/trackDb/epdNewPromoter.html @@ -10,33 +10,38 @@ <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 +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> +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"