c1bf92e8d0500957bef941593240f66eabe8094d
kate
  Wed May 13 10:30:24 2020 -0700
Polish track description and generalize to include mouse. Add 4-char labels for classification  and abbreviated accession label as per JK. Filter on the more user-friendly classification labels. refs #24668

diff --git src/hg/makeDb/trackDb/encodeCcreCombined.html src/hg/makeDb/trackDb/encodeCcreCombined.html
index 813681f..b359eef 100644
--- src/hg/makeDb/trackDb/encodeCcreCombined.html
+++ src/hg/makeDb/trackDb/encodeCcreCombined.html
@@ -1,76 +1,89 @@
 <h2>Description</h2>
 <p>
-This track displays the <em>ENCODE Registry of candidate cis-Regulatory Elements</em> (cCREs) in
-the human genome, a total of 926,535 elements identified and classified by the 
-ENCODE Data Analysis Center according to regulatory effect.
-cCREs are the subset of DNase hypersensitivity sites clustered across all ENCODE samples
+This track displays the <em>ENCODE Registry of candidate cis-Regulatory Elements</em> (cCREs) 
+in the genome, identified and classified by the ENCODE Data Analysis Center according to 
+regulatory effect.
+CCREs are the subset of DNase hypersensitivity sites clustered across all samples
 that are supported by either histone modifications (H3K4me3 and H3K27ac) or CTCF-binding data.
 The cCRE dataset is the core of the integrative level of epigenomic and transcriptomic
 annotations produced by ENCODE.
+The registry currently comprises a total of 926,535 elements in the human genome and 339,815 
+in the mouse genome (less comprehensively assayed).
 </p>
 Additional exploration of the cCRE's and underlying raw ENCODE data is provided by the
 <a target="_blank" href="https://screen.wenglab.org/">
 SCREEN</a>
 (Search Candidate cis-Regulatory Elements) web tool,
-designed specifically for the registry, accessible by linkouts from the track details page.
+designed specifically for the registry, and accessible by linkouts from the track details page.
 
 <!--
 <p>
 The related cCREs by Biosample composite track presents ccREs 
 and associated epigenetic signal in all individual biosamples in a large matrix.
 Additional views of the data are provided by the <a>ENCODE Integrative Megahub</a>.
 </p>
 -->
 
 <h2>Display Conventions and Configuration</h2>
 <p>
-CCREs are colored according to classification by regulatory signature:
+CCREs are colored and labeled according to classification by regulatory signature:
 <p>
 <table cellpadding='2'>
   
   <tr>
     <th style="border-bottom: 2px solid;">Color</th>
     <th style="border-bottom: 2px solid;"></th>
-    <th style="border-bottom: 2px solid;">Group</th>
+    <th style="border-bottom: 2px solid;">Label</th>
+    <th style="border-bottom: 2px solid;">Classification</th>
     <th style="border-bottom: 2px solid;"></th>
   </tr>
   </thead>
 
 <tr><td style='background-color: red;'></td><td>red</td>
+        <td>prom</td>
         <td>promoter-like</td>
         <td>PLS</td></tr>
 <tr><td style='background-color: orange;'></td><td>orange</td>
+        <td>enhP</td>
         <td>proximal enhancer-like</td>
         <td>pELS</td></tr>
 <tr><td style='background-color: yellow;'></td><td>yellow</td>
+        <td>enhD</td>
         <td>distal enhancer-like</td>
         <td>dELS</td></tr>
 <tr><td style='background-color: blue;'</td><td>blue</td>
+        <td>CTCF</td>
         <td>CTCF-only</td>
         <td>CTCF-only</td></tr>
 <tr><td style='background-color: #ffa0a0;'></td><td>pink</td>
+        <td>K4m3</td>
         <td>DNase-H3K4me3</td>
         <td>DNase-H3K4me3</td></tr>
 </table>
 </p>
+<p>
+The DNase-H3K4me3 elements are those with promoter-like biochemical signature that
+are not within 200bp of an annotated TSS.
+</p>
 
 <h2>Methods</h2>
 <p>
-All individual DNase hypsersensitivity sites (DHSs) identified from 706 DNAse-seq experiments
-in human (a total of 93 million) were iteratively clustered and filtered 
-for highest signal across all experiments, producing 2.2 million representative DHSs (rDHSs).
+All individual DNase hypsersensitivity sites (DHSs) identified from DNAse-seq experiments
+(in human, a total of 93 million sites from 706 experiments) were iteratively clustered
+and filtered for highest signal across all experiments, producing 
+representative DHSs (rDHSs), with a total of  2.2 million such sites in human.
 The highest signal elements from this set that were also supported by high H3K4me3, H3K27ac 
 and/or CTCF ChIP-seq signals were designated cCRE's (a total of 926,535 in human).
 </p>
 <p>
 Classification of cCRE's was performed based on the following criteria:
 <p>
 <p>
 1. cCREs with promoter-like signatures (cCRE-PLS) fall within 200 bp of 
 an annotated GENCODE TSS and have high DNase and H3K4me3 signals.
 </p>
 <p>
 2. cCREs with enhancer-like signatures (cCRE-ELS) have high DNase and H3K27ac 
 with low H3K4me3 max-Z score if they are within 200 bp of an annotated TSS. 
 The subset of cCREs-ELS within 2 kb of a TSS is denoted proximal (cCRE-pELS), 
 while the remaining subset is denoted distal (cCRE-dELS).