7648a54276c90c08ff73dc555fe051f92dd4f57d
gperez2
  Sun Mar 8 18:20:00 2026 -0700
Updating the Methylation Atlas summary subtracks section and adding a Cell/Tissue Type section, #36826

diff --git src/hg/makeDb/trackDb/human/methylationAtlas.html src/hg/makeDb/trackDb/human/methylationAtlas.html
index de38a0ac535..4f318dc08c4 100755
--- src/hg/makeDb/trackDb/human/methylationAtlas.html
+++ src/hg/makeDb/trackDb/human/methylationAtlas.html
@@ -2,37 +2,42 @@
 <p>
 The <b>Human Methylation Atlas</b> tracks display genome-wide DNA methylation profiles from 
 deep whole-genome bisulfite sequencing (WGBS) of <b>39 primary human cell types</b> 
 sorted from 205 healthy tissue samples. This comprehensive resource enables fragment-level 
 analysis across thousands of unique markers, providing a detailed reference for 
 cell-type-specific methylation patterns.
 </p>
 
 <b>Human Methylation Atlas Summary</b> consists of the following subtracks:
 <ul>
   <li><b>All unmethylated regions</b> track displays a comprehensive catalogue of unmethylated
 	  genomic regions identified independently for each of the 39 cell types in the atlas
 	  using a fragment-level analysis, retaining regions where at least 85% of sequenced DNA
 	  fragments covering four or more CpGs are unmethylated.</li><br>
   <li><b>Putative enhancers from unmethylated regions</b> track displays a genome-wide catalogue of
-	  putative transcriptional enhancers for each of the 39 cell types, derived from regions
-	  where at least 85% of sequenced DNA fragments are unmethylated and that overlap H3K27ac
-	  but not H3K4me3 ChIP-seq peaks, distinguishing distal enhancer elements from active
-	  promoters.</li><br>
+	  putative transcriptional enhancers derived from regions where at least 85% of sequenced
+	  DNA fragments are unmethylated, and that overlap H3K27ac but not H3K4me3 ChIP-seq peaks,
+	  distinguishing distal enhancer elements from active promoters. This track covers 32 of
+	  the 39 cell types, as H3K27ac ChIP-seq data were unavailable for Adipocytes, Bone
+	  Osteoblasts, Erythrocyte Progenitors, Fallopian Epithelium, Gallbladder, Ovary Epithelium,
+	  and Smooth Muscle. </li><br>
   <li><b>Top 250 unmethylated regions specific to each cell type</b> track displays the top 250
 	  genomic regions most specifically unmethylated in each of the 39 cell types, identified
-	  using a one-versus-all comparison approach.</li>
+	  using a one-versus-all comparison approach. Some regions are shared across closely related
+	  cell types (for example, Neuron:Oligodend or Colon-Ep:Gastric-Ep:Small-Int-Ep),
+	  indicating they are unmethylated across those cell types but methylated in all others in
+	  the atlas.</li>
 </ul>
 <p>
 Unsupervised clustering of these methylomes recapitulates key elements of tissue ontogeny and
 developmental lineage relationships.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 
 <h3>Track Colors</h3>
 <p>
 Tracks are colored by tissue/cell type category as follows:
 </p>
 
 <table border="1" cellpadding="4" cellspacing="0">
 <tr><th>Color</th><th>Cell Type(s)</th></tr>
@@ -65,30 +70,41 @@
 <tr><td style="background-color:rgb(100,149,237);width:30px;">&nbsp;</td><td>Lung Bronchus Epithelium</td></tr>
 <tr><td style="background-color:rgb(135,206,250);width:30px;">&nbsp;</td><td>Lung Alveolar Epithelium</td></tr>
 <tr><td style="background-color:rgb(255,140,105);width:30px;">&nbsp;</td><td>Kidney Epithelium</td></tr>
 <tr><td style="background-color:rgb(255,105,180);width:30px;">&nbsp;</td><td>Endothelial</td></tr>
 <tr><td style="background-color:rgb(219,112,147);width:30px;">&nbsp;</td><td>Breast Basal Epithelium</td></tr>
 <tr><td style="background-color:rgb(255,182,193);width:30px;">&nbsp;</td><td>Breast Luminal Epithelium</td></tr>
 <tr><td style="background-color:rgb(218,112,214);width:30px;">&nbsp;</td><td>Fallopian Epithelium</td></tr>
 <tr><td style="background-color:rgb(221,160,221);width:30px;">&nbsp;</td><td>Ovary Epithelium</td></tr>
 <tr><td style="background-color:rgb(210,180,140);width:30px;">&nbsp;</td><td>Adipocytes</td></tr>
 <tr><td style="background-color:rgb(222,184,135);width:30px;">&nbsp;</td><td>Epidermal Keratinocytes</td></tr>
 <tr><td style="background-color:rgb(245,222,179);width:30px;">&nbsp;</td><td>Dermal Fibroblasts</td></tr>
 <tr><td style="background-color:rgb(188,143,143);width:30px;">&nbsp;</td><td>Bone Osteoblasts</td></tr>
 <tr><td style="background-color:rgb(0,206,209);width:30px;">&nbsp;</td><td>Head Neck Epithelium</td></tr>
 </table>
 
+<p>
+Items in these tracks can be filtered by:
+</p>
+<ul>
+  <li><b>Cell/Tissue Type</b> - The cell or tissue type associated with each region.
+  Filter values include the 39 cell types for the <b>All Unmethylated Regions</b> track,
+  32 cell types for the <b>Putative Enhancers</b> track, and 39 cell types plus combined
+  cell type groups for the <b>Top 250 Unmethylated Regions</b> track. The default is no
+  filtering.</li>
+</ul>
+
 <h2>Methods</h2>
 
 <h3>Sample Collection and Sequencing</h3>
 <p>
 Primary human cells were isolated from freshly dissociated adult healthy tissues using 
 fluorescence-activated cell sorting (FACS), yielding high-purity preparations across major 
 cell lineages. A total of 205 samples representing 77 primary cell types were collected from
 137 consenting donors and merged into 39 cell type groups based on methylation similarity.
 Average sample purity exceeded 90% as determined by flow cytometry, gene expression, and
 DNA methylation analysis. Some cell types showed lower purity, including colon fibroblasts (78%),
 smooth muscle cells (82%), endothelial cells (86%), and adipocytes (87%).
 </p>
 
 <p>
 Several cell types are absent from the atlas, typically due to limited availability of primary