914524d3334b7ccffbf791474cbdd8b8e331b57a brianlee Mon May 23 14:54:27 2022 -0700 Adding an image of working filters on ReMap, as they are cool, good to add in Progress Report and NAR paper refs #28960 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 78a9e55..6689a5c 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -239,30 +239,41 @@ <p> We are happy to announce the release of the ReMap Atlas of Regulatory Regions track for <a href="/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=ReMap">hg38</a>, <a href="/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=ReMap">hg19</a>, <a href="/cgi-bin/hgTrackUi?db=mm39&c=chrX&g=ReMap">mm39</a>, <a href="/cgi-bin/hgTrackUi?db=mm10&c=chrX&g=ReMap">mm10</a>, and <a href="/cgi-bin/hgTrackUi?db=dm6&c=chr4&g=ReMap">dm6</a>. These tracks represent the <a href="https://remap.univ-amu.fr/" target="_blank">ReMap Atlas</a> of regulatory regions, which consists of a large-scale integrative analysis of all Public ChIP-seq data for transcriptional regulators from GEO, ArrayExpress, and ENCODE. Each transcription factor follows a specific RGB color. Individual BED files for specific TFs, cells/biotypes, or data sets can be found and downloaded on the <a href="https://remap.univ-amu.fr/download_page" target="_blank">ReMap website</a>. </p> <p> +The below image shows the ReMap ChIP-seq Track, where a right-click can bring up the configuration +option. Then there are filters available using either regular expression (regexp) or wildcards. +In the image <code>.*A\|B\|F.*</code> is using regexp, which will select all Transcriptional +regulators that include either the letter A, B, or F, while a separate wildcard filter on the +Biotypes field, <code>MC*</code>, selects all tissue names starting with MC.</p> Drop-down menus +also exist to perform the same filters, as well as the ability to customize the label, for instance, +to only show the Biotype.</p> +<div class="text-center"> + <img src="../images/newsArchImages/ReMap.png" alt="ReMap Filter" width="700"> +</div> +<p> We would like to thank Benoit Ballester and the ReMap team at <a href="https://tagc.univ-amu.fr/" target="_blank">TAGC INSERM</a> (Inserm National Institute of Health and Medical Research) for making this data available. We also want to thank Max Haeussler, Gerardo Perez and Jairo Navarro for the creation and release of these tracks. </p> <a name="042222"></a> <h2>Apr. 22, 2022 European Variant Archive (EVA) data now available on 16 assemblies</h2> <p> The <a href="https://www.ebi.ac.uk/eva/" target="_blank">European Variant Archive</a> has extensive data on variation across many different species and assemblies. We have updated our 16 most popular non-human genome assemblies with their latest data: <a href="https://www.ebi.ac.uk/eva/?RS-Release&releaseVersion=3" target="_blank">Release 3</a>. Adding more to this dataset, we processed the raw data to include two extra fields, describing variant class and amino acid change if present. You can read more about these datasets on