0b65049e315263b6d6c7a46f3f5c2894a8413e8c
lrnassar
  Wed Apr 8 16:13:38 2026 -0700
Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923

hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data.
The Weng lab fixed a bug where both variants pointed to the same file. Now
83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files,
80 former fake tissue-only subtracks converted to all-biosamples, and the
DNase nose organ added / lymphoid tissue all-biosamples removed to match hub.

Default subtracks changed from cell lines to tissue samples per Weng lab
request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver
postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks.

Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166),
mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added
ENCODE color mapping wiki link to all 12 multiWig HTML description pages.

Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison).
mm10 supertrack developer list corrected (removed Greg Andrews per hub).

ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages
updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant
assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).

diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra
index fe4044364e6..89663724f28 100644
--- src/hg/makeDb/trackDb/relatedTracks.ra
+++ src/hg/makeDb/trackDb/relatedTracks.ra
@@ -29,32 +29,32 @@
 hg38 ReMap liftHg19 NCBI ReMap, even though it has the same name, is a liftOver-like hg19/hg38 alignment, and unrelated to the ReMap database
 hg38 liftHg19 ReMap ReMap, even though it has the same name, is a database of transcription factor binding sites, unrelated to NCBI ReMap
 
 hg38 ReMap jaspar JASPAR is a database of predicted TF binding sites, based on short DNA matches. Unlike ReMap, the data is purely computational.
 
 hg38 jaspar ReMap ReMap is a database of TF binding sites inferred from ChIP-Seq Data. Unlike JASPAR predictions, these sites are supported by functional assay
 
 hg38 problematic mappability The mappability track contains regions where short sequencing reads are hard to align
 hg38 mappability problematic The problematic regions track contains various gene clusters and the ENCODE blacklist
 hg38 problematic grcIncidentDb The GRC (Genome Reference Consortium) incidents track contains regions that were flagged by the group that puts together the genome 
 hg38 grcIncidentDb problematic The problematic regions track lists unusual regions and the ones that often lead to artefacts when aligning reads to the reference genome
 
 hg38 phasedVars varFreqs The variant frequencies track contains projects where variant frequencies, aka allele frequencies, are publicly available.
 hg38 varFreqs phasedVars The phased variants track contains projects that provide haplotype-phased genotypes/variants.
 
-hg38 wgEncodeReg4 wgEncodeReg ENCODE4 update of ENCODE3 Regulation
-hg38 wgEncodeReg wgEncodeReg4 ENCODE4 update of ENCODE3 Regulation
+hg38 wgEncodeReg4 wgEncodeReg Previous ENCODE3 Regulation track
+hg38 wgEncodeReg wgEncodeReg4 New ENCODE4 Regulation track
 hg38 wgEncodeReg4 cCREs Related ENCODE4 cCRE annotations
 hg38 cCREs wgEncodeReg4 Related ENCODE4 regulation data
 
 # hg19:
 hg19 caddSuper gnomad View associated variants
 hg19 gnomad caddSuper View CADD scores for this variant and region
 
 hg19 decipherHaploIns gnomadPLI Compare haploinsufficiency metrics as defined by gnomAD
 hg19 gnomadPLI decipherHaploIns Compare constraint metrics as defined by DECIPHER
 
 hg19 revel caddSuper CADD, a similar deleteriousness score, and not used as an input by REVEL
 hg19 caddSuper revel REVEL, a similar deleteriousness score
 
 hg19 liftHg38 grcIncidentDb GRC Incident database, to explore reasons why the assembly was changed
 hg19 grcIncidentDb liftHg38 LiftOver alignments between hg38 and hg38 to explore how the GRC incident assembly changes affect whole-genome alignments between hg19 and hg38 used for lifting data from hg19
@@ -71,19 +71,19 @@
 hg19 ReMap liftHg38 NCBI ReMap, even though it has the same name, is a liftOver-like hg19/hg38 alignment, and unrelated to the ReMap database
 hg19 liftHg38 ReMap ReMap, even though it has the same name, is a database of transcription factor binding sites, unrelated to NCBI ReMap
 
 hg19 refSeqComposite pseudoYale60 NCBI RefSeq Curated and RefSeq Other contains pseudogenes, but the Yale annotation should be more comprehensive for this transcript type
 hg19 pseudoYale60 refSeqComposite NCBI RefSeq Curated and RefSeq Other also contain some transcribed and untranscribed pseudogenes, respectively.
 
 hg19 constraintSuper gnomadPLI Predicted constraint metrics from gnomAD
 hg19 gnomadPLI constraintSuper Container track of various constraint scores
 
 # mm39:
 
 mm39 knownGene knownGeneArchive View previous versions of GENCODE Genes
 mm39 knownGeneArchive knownGene View the latest GENCODE Genes version
 
 # mm10 ENCODE4 Regulation:
-mm10 encode4Reg encode3Reg ENCODE4 update of ENCODE3 Regulation
-mm10 encode3Reg encode4Reg ENCODE4 update of ENCODE3 Regulation
+mm10 encode4Reg encode3Reg Previous ENCODE3 Regulation track
+mm10 encode3Reg encode4Reg New ENCODE4 Regulation track
 mm10 encode4Reg cCREs Related ENCODE4 cCRE annotations
 mm10 cCREs encode4Reg Related ENCODE4 regulation data