b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 gperez2 Wed Sep 30 14:17:50 2026 -0700 Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599 diff --git src/hg/makeDb/trackDb/human/hg38/tad.ra src/hg/makeDb/trackDb/human/hg38/tad.ra index 29edc39bfb1..d93a791ba42 100644 --- src/hg/makeDb/trackDb/human/hg38/tad.ra +++ src/hg/makeDb/trackDb/human/hg38/tad.ra @@ -39,245 +39,245 @@ track tadsSchmitt parent tads priority 4 compositeTrack on shortLabel Schmitt 2016 boundaries longLabel TAD boundaries across 21 human tissues and cell lines (Schmitt et al. 2016) type bigBed 4 group regulation visibility hide html tadsSchmitt subGroup1 stype Sample_type cellLine=Cell_line tissue=Primary_tissue subGroup2 organ Organ_system brain=Brain cardiovascular=Cardiovascular immune=Immune digestive=Digestive endocrine=Endocrine reproductive=Reproductive muscle=Muscle respiratory=Respiratory urinary=Urinary stem=Stem dimensions dimX=organ dimY=stype sortOrder stype=+ organ=+ showSubtrackColorOnUi on -allButtonPair on track tadsSchmittGM12878 parent tadsSchmitt on - shortLabel GM12878 bnd + shortLabel GM12878 longLabel TAD boundaries in GM12878 lymphoblastoid cells (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittGM12878.bb subGroups stype=cellLine organ=immune color 51,160,44 mouseOver Sample: GM12878 lymphoblastoid cells (TAD boundary, 40 kb bin) track tadsSchmittH1 parent tadsSchmitt on - shortLabel H1-hESC bnd + shortLabel H1-hESC longLabel TAD boundaries in H1 human embryonic stem cells (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittH1.bb subGroups stype=cellLine organ=stem color 152,78,163 mouseOver Sample: H1 human embryonic stem cells (TAD boundary, 40 kb bin) track tadsSchmittIMR90 parent tadsSchmitt on - shortLabel IMR90 bnd + shortLabel IMR90 longLabel TAD boundaries in IMR90 fetal lung fibroblasts (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittIMR90.bb subGroups stype=cellLine organ=respiratory color 178,150,40 mouseOver Sample: IMR90 fetal lung fibroblasts (TAD boundary, 40 kb bin) track tadsSchmittMES parent tadsSchmitt off - shortLabel Mesendoderm bnd + shortLabel Mesendoderm longLabel TAD boundaries in H1-derived mesendoderm cells (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittMES.bb subGroups stype=cellLine organ=stem color 152,78,163 mouseOver Sample: H1-derived mesendoderm cells (TAD boundary, 40 kb bin) track tadsSchmittMSC parent tadsSchmitt off - shortLabel Mesench SC bnd + shortLabel Mesenchymal SC longLabel TAD boundaries in H1-derived mesenchymal stem cells (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittMSC.bb subGroups stype=cellLine organ=stem color 152,78,163 mouseOver Sample: H1-derived mesenchymal stem cells (TAD boundary, 40 kb bin) track tadsSchmittNPC parent tadsSchmitt off - shortLabel Neural prog bnd + shortLabel Neural progenitor longLabel TAD boundaries in H1-derived neural progenitor cells (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittNPC.bb subGroups stype=cellLine organ=stem color 152,78,163 mouseOver Sample: H1-derived neural progenitor cells (TAD boundary, 40 kb bin) track tadsSchmittTRO parent tadsSchmitt off - shortLabel Trophoblast bnd + shortLabel Trophoblast longLabel TAD boundaries in H1-derived trophoblast-like cells (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittTRO.bb subGroups stype=cellLine organ=stem color 152,78,163 mouseOver Sample: H1-derived trophoblast-like cells (TAD boundary, 40 kb bin) track tadsSchmittAD parent tadsSchmitt off - shortLabel Adrenal bnd + shortLabel Adrenal longLabel TAD boundaries in adrenal gland (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittAD.bb subGroups stype=tissue organ=endocrine color 31,120,180 mouseOver Sample: adrenal gland (TAD boundary, 40 kb bin) track tadsSchmittAO parent tadsSchmitt off - shortLabel Aorta bnd + shortLabel Aorta longLabel TAD boundaries in aorta (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittAO.bb subGroups stype=tissue organ=cardiovascular color 227,26,28 mouseOver Sample: aorta (TAD boundary, 40 kb bin) track tadsSchmittBL parent tadsSchmitt off - shortLabel Bladder bnd + shortLabel Bladder longLabel TAD boundaries in bladder (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittBL.bb subGroups stype=tissue organ=urinary color 251,154,153 mouseOver Sample: bladder (TAD boundary, 40 kb bin) track tadsSchmittCO parent tadsSchmitt on - shortLabel Cortex bnd + shortLabel Cortex longLabel TAD boundaries in dorsolateral prefrontal cortex (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittCO.bb subGroups stype=tissue organ=brain color 106,61,154 mouseOver Sample: dorsolateral prefrontal cortex (TAD boundary, 40 kb bin) track tadsSchmittHC parent tadsSchmitt off - shortLabel Hippocampus bnd + shortLabel Hippocampus longLabel TAD boundaries in hippocampus (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittHC.bb subGroups stype=tissue organ=brain color 106,61,154 mouseOver Sample: hippocampus (TAD boundary, 40 kb bin) track tadsSchmittLG parent tadsSchmitt off - shortLabel Lung bnd + shortLabel Lung longLabel TAD boundaries in lung (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittLG.bb subGroups stype=tissue organ=respiratory color 178,150,40 mouseOver Sample: lung (TAD boundary, 40 kb bin) track tadsSchmittLI parent tadsSchmitt on - shortLabel Liver bnd + shortLabel Liver longLabel TAD boundaries in liver (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittLI.bb subGroups stype=tissue organ=digestive color 255,127,0 mouseOver Sample: liver (TAD boundary, 40 kb bin) track tadsSchmittLV parent tadsSchmitt off - shortLabel Left ventricle bnd + shortLabel Left ventricle longLabel TAD boundaries in left ventricle of heart (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittLV.bb subGroups stype=tissue organ=cardiovascular color 227,26,28 mouseOver Sample: left ventricle of heart (TAD boundary, 40 kb bin) track tadsSchmittOV parent tadsSchmitt off - shortLabel Ovary bnd + shortLabel Ovary longLabel TAD boundaries in ovary (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittOV.bb subGroups stype=tissue organ=reproductive color 177,89,40 mouseOver Sample: ovary (TAD boundary, 40 kb bin) track tadsSchmittPA parent tadsSchmitt off - shortLabel Pancreas bnd + shortLabel Pancreas longLabel TAD boundaries in pancreas (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittPA.bb subGroups stype=tissue organ=endocrine color 31,120,180 mouseOver Sample: pancreas (TAD boundary, 40 kb bin) track tadsSchmittPO parent tadsSchmitt off - shortLabel Psoas muscle bnd + shortLabel Psoas muscle longLabel TAD boundaries in psoas muscle (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittPO.bb subGroups stype=tissue organ=muscle color 120,180,200 mouseOver Sample: psoas muscle (TAD boundary, 40 kb bin) track tadsSchmittRV parent tadsSchmitt off - shortLabel Right ventricle bnd + shortLabel Right ventricle longLabel TAD boundaries in right ventricle of heart (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittRV.bb subGroups stype=tissue organ=cardiovascular color 227,26,28 mouseOver Sample: right ventricle of heart (TAD boundary, 40 kb bin) track tadsSchmittSB parent tadsSchmitt off - shortLabel Small bowel bnd + shortLabel Small bowel longLabel TAD boundaries in small bowel (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittSB.bb subGroups stype=tissue organ=digestive color 255,127,0 mouseOver Sample: small bowel (TAD boundary, 40 kb bin) track tadsSchmittSX parent tadsSchmitt off - shortLabel Spleen bnd + shortLabel Spleen longLabel TAD boundaries in spleen (Schmitt et al. 2016) type bigBed 4 bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittSX.bb subGroups stype=tissue organ=immune color 51,160,44 mouseOver Sample: spleen (TAD boundary, 40 kb bin) track tadsMcArthur parent tads priority 5 shortLabel TAD boundary stability longLabel TAD boundary stability across 37 cell-type maps (McArthur & Capra 2021) type bigBed 5 + 2 bigDataUrl /gbdb/$D/bbi/tad/tadsMcArthur.bb group regulation visibility hide spectrum on filter.contexts 4:37 filterByRange.contexts on filterLimits.contexts 1:37 -filterLabel.contexts Minimum number of cell-type maps sharing the boundary (1-37) -mouseOver Boundary recurrent: $contexts / 37 cell-type maps
Percentile: $percentile +filterLabel.contexts Number of cell-type maps sharing the boundary +labelFields none +mouseOver Boundary recurrent: $contexts / 37 cell-type maps
Stability percentile (0-1): $percentile html tadsMcArthur include tads3dgb.ra