b4808fac05f88a0170f2642a1670d571ceca4b7e
gperez2
  Mon May 4 10:08:39 2026 -0700
Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923

- Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page.
- Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis).
- Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings.
- Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding.
- Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology.
- Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions.
- Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.

diff --git src/hg/makeDb/trackDb/encode4RegLayeredDisplay.shared.html src/hg/makeDb/trackDb/encode4RegLayeredDisplay.shared.html
new file mode 100644
index 00000000000..4f516c2653a
--- /dev/null
+++ src/hg/makeDb/trackDb/encode4RegLayeredDisplay.shared.html
@@ -0,0 +1,12 @@
+<h2>Display Conventions and Configuration</h2>
+<p>
+This track uses a transparent overlay to visualize data from multiple organs or tissues within
+the same vertical space. For each organ or tissue, signals from all associated experiments were
+averaged to generate the displayed track. Each organ or tissue is assigned a distinct
+color following the
+<a href="https://wiki.wenglab.org/references/color-mappings/" target="_blank">ENCODE color
+mapping convention</a>,
+selected to be light and saturated to maintain clarity when overlaid. Initially, each layered
+track displays an overlay of five representative organs: blood, brain, kidney, liver, and
+muscle. Clicking on the track opens a details page where you can view and select organs or
+tissues.</p>