8a3f24f0e70e94dc4812283bbd60c715651d6c46
lrnassar
  Mon Nov 3 14:50:27 2025 -0800
Staging the ENCODE4 cCREs track. Next step is asking for feedback from the authors, refs #34923

diff --git src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
index b4d0a07bc9f..2191e08d790 100644
--- src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
+++ src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
@@ -1,27 +1,33 @@
 track cCREs
 superTrack on show
-shortLabel ENCODE cCREs ALPHA 
+shortLabel ENCODE cCREs
 longLabel ENCODE Registry of cCREs (candidate Cis-Regulatory Elements) 
 group regulation
-canPack On
 priority 1
 pennantIcon New red ../goldenPath/newsarch.html#XXXXXX "XXX"
+html cCREsSuper.html
 
 track encodeCcreCombined override
-superTrack cCREs hide
+parent cCREs
+longLabel ENCODE3 combined Candidate Cis-Regulatory Elements (cCREs) from all samples
+priority 3
+visibility hide
+shortLabel ENCODE3 cCREs
+pennantIcon snowflake.png ../goldenPath/newsarch.html#XXXXXX "This data represents ENCODE3 cCREs. For the latest data, see the ENCODE4 cCREs track."
 
 track cCREregistry
-shortLabel cCRE Registry
-longLabel Candidate cis-regulatory elements (cCREs) from the ENCODE Registry
+shortLabel ENCODE4 cCREs
+longLabel ENCODE4 combined Candidate Cis-Regulatory Elements (cCREs) from all samples
 type bigBed 9 + 5
 bigDataUrl /gbdb/$D/encode4/ccre/encodeCcreRegistry.bb
 visibility dense
-maxHeightPixels 50
 priority 1
 filterValues.cCRE_class CA|Chromatin accessibility (CA),CA-CTCF|Chromatin accessibility + CTCF (CA-CTCF),CA-H3K4me3|Chromatin accessibility + H3K4me3 (CA-H3K4me3),CA-TF|Chromatin accessibility + transcription factor (CA-TF),dELS|TSS-distal enhancer-like signatures (distal enhancer),pELS|TSS-proximal enhancer-like signatures (proximal enhancer),PLS|Promoter-like signatures (promoter),TF|Transcription factor (TF)
-superTrack cCREs show
+parent cCREs
 filterType.cCRE_class multipleListOr
-mouseOver <b>ID:</b> ${name}<br><b>Class:</b> ${cCRE_class}
-url https://screen.wenglab.org/search?assembly=GRCh38&accessions=$$&page=2
+mouseOver <b>ID:</b> <a target="_blank" href="https://screen.wenglab.org/search?assembly=GRCh38&accessions=${name}">${name}</a><br><b>Class:</b> ${cCRE_class}<br><b>DNase Max-Z:</b> ${DNase_maxZ}<br><b>H3K4me3 Max-Z:</b> ${H3K4me3_maxZ}<br><b>H3K27ac Max-Z:</b> ${H3K27ac_maxZ}<br><b>CTCF Max-Z:</b> ${CTCF_maxZ}
+url https://screen.wenglab.org/search?assembly=GRCh38&accessions=$$
 urlLabel cCRE details on SCREEN:
-html ccre.html
+dataVersion ENCODE Registry version 4, 2024. (ENCODE4 data includes ENCODE2 and ENCODE3)
+
+include encode4.ccres.ra