17b7d3c37be41135afaf8e91e365e3847af96ca5 lrnassar Mon Jun 22 10:56:56 2026 -0700 Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt). diff --git src/hg/makeDb/trackDb/human/hg38/tad.ra src/hg/makeDb/trackDb/human/hg38/tad.ra new file mode 100644 index 00000000000..0b7451c5bd0 --- /dev/null +++ src/hg/makeDb/trackDb/human/hg38/tad.ra @@ -0,0 +1,283 @@ +track tads +superTrack on hide +shortLabel TADs +longLabel Topologically associating domains (TADs) and boundaries from Hi-C studies +group regulation +html tads + +track tadsDixon +parent tads +priority 1 +compositeTrack on +shortLabel Dixon 2012 TADs +longLabel TAD domains in hESC and IMR90 cells (Dixon et al. 2012, lifted from hg18) +type bigBed 4 +group regulation +visibility pack +html tadsDixon + + track tadsDixonHESC + parent tadsDixon on + shortLabel hESC TADs + longLabel TAD domains in H1 human embryonic stem cells (Dixon et al. 2012) + type bigBed 4 + bigDataUrl /gbdb/$D/bbi/tad/tadsDixonHESC.bb + color 27,158,119 + mouseOver Cell type: $name (TAD domain) + + track tadsDixonIMR90 + parent tadsDixon on + shortLabel IMR90 TADs + longLabel TAD domains in IMR90 fetal lung fibroblasts (Dixon et al. 2012) + type bigBed 4 + bigDataUrl /gbdb/$D/bbi/tad/tadsDixonIMR90.bb + color 217,95,2 + mouseOver Cell type: $name (TAD domain) + +include tadsEncode.ra + +track tadsSchmitt +parent tads +priority 4 +compositeTrack on +shortLabel Schmitt 2016 boundaries +longLabel TAD boundaries across 21 human tissues and cell lines (Schmitt et al. 2016) +type bigBed 4 +group regulation +visibility hide +html tadsSchmitt +subGroup1 stype Sample_type cellLine=Cell_line tissue=Primary_tissue +subGroup2 organ Organ_system brain=Brain cardiovascular=Cardiovascular immune=Immune digestive=Digestive endocrine=Endocrine reproductive=Reproductive muscle=Muscle respiratory=Respiratory urinary=Urinary stem=Stem +dimensions dimX=organ dimY=stype +sortOrder stype=+ organ=+ +showSubtrackColorOnUi on +allButtonPair on + + track tadsSchmittGM12878 + parent tadsSchmitt on + shortLabel GM12878 bnd + longLabel TAD boundaries in GM12878 lymphoblastoid cells (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$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 + longLabel TAD boundaries in H1 human embryonic stem cells (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittH1.bb + subGroups stype=cellLine organ=stem + color 152,78,163 + mouseOver Sample: H1 human embryonic stem cells (TAD boundary, 40 kb bin) + + track tadsSchmittIMR90 + parent tadsSchmitt on + shortLabel IMR90 bnd + longLabel TAD boundaries in IMR90 fetal lung fibroblasts (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$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 + longLabel TAD boundaries in H1-derived mesendoderm cells (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittMES.bb + subGroups stype=cellLine organ=stem + color 152,78,163 + mouseOver Sample: H1-derived mesendoderm cells (TAD boundary, 40 kb bin) + + track tadsSchmittMSC + parent tadsSchmitt off + shortLabel Mesench SC bnd + longLabel TAD boundaries in H1-derived mesenchymal stem cells (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$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 + longLabel TAD boundaries in H1-derived neural progenitor cells (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittNPC.bb + subGroups stype=cellLine organ=stem + color 152,78,163 + mouseOver Sample: H1-derived neural progenitor cells (TAD boundary, 40 kb bin) + + track tadsSchmittTRO + parent tadsSchmitt off + shortLabel Trophoblast bnd + longLabel TAD boundaries in H1-derived trophoblast-like cells (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$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 + longLabel TAD boundaries in adrenal gland (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittAD.bb + subGroups stype=tissue organ=endocrine + color 31,120,180 + mouseOver Sample: adrenal gland (TAD boundary, 40 kb bin) + + track tadsSchmittAO + parent tadsSchmitt off + shortLabel Aorta bnd + longLabel TAD boundaries in aorta (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$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 + longLabel TAD boundaries in bladder (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittBL.bb + subGroups stype=tissue organ=urinary + color 251,154,153 + mouseOver Sample: bladder (TAD boundary, 40 kb bin) + + track tadsSchmittCO + parent tadsSchmitt on + shortLabel Cortex bnd + longLabel TAD boundaries in dorsolateral prefrontal cortex (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$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 + longLabel TAD boundaries in hippocampus (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittHC.bb + subGroups stype=tissue organ=brain + color 106,61,154 + mouseOver Sample: hippocampus (TAD boundary, 40 kb bin) + + track tadsSchmittLG + parent tadsSchmitt off + shortLabel Lung bnd + longLabel TAD boundaries in lung (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$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 + longLabel TAD boundaries in liver (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittLI.bb + subGroups stype=tissue organ=digestive + color 255,127,0 + mouseOver Sample: liver (TAD boundary, 40 kb bin) + + track tadsSchmittLV + parent tadsSchmitt off + shortLabel Left ventricle bnd + longLabel TAD boundaries in left ventricle of heart (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$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 + longLabel TAD boundaries in ovary (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittOV.bb + subGroups stype=tissue organ=reproductive + color 177,89,40 + mouseOver Sample: ovary (TAD boundary, 40 kb bin) + + track tadsSchmittPA + parent tadsSchmitt off + shortLabel Pancreas bnd + longLabel TAD boundaries in pancreas (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$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 + longLabel TAD boundaries in psoas muscle (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittPO.bb + subGroups stype=tissue organ=muscle + color 120,180,200 + mouseOver Sample: psoas muscle (TAD boundary, 40 kb bin) + + track tadsSchmittRV + parent tadsSchmitt off + shortLabel Right ventricle bnd + longLabel TAD boundaries in right ventricle of heart (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$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 + longLabel TAD boundaries in small bowel (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittSB.bb + subGroups stype=tissue organ=digestive + color 255,127,0 + mouseOver Sample: small bowel (TAD boundary, 40 kb bin) + + track tadsSchmittSX + parent tadsSchmitt off + shortLabel Spleen bnd + longLabel TAD boundaries in spleen (Schmitt et al. 2016) + type bigBed 4 + bigDataUrl /gbdb/$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 in $contexts of 37 cell-type maps (percentile $percentile) +html tadsMcArthur + +include tads3dgb.ra