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/mouse/mm10/tadsEncode.ra src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.ra new file mode 100644 index 00000000000..36f3b31ea15 --- /dev/null +++ src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.ra @@ -0,0 +1,176 @@ +track tadsEncode +parent tads +priority 2 +compositeTrack faceted +shortLabel ENCODE TADs +longLabel ENCODE contact domains (TADs) across 16 mouse biosamples (Arrowhead/Hi-C) +type bigBed 4 + 5 +group regulation +visibility pack +metaDataUrl /gbdb/mm10/bbi/tad/tadsEncode_metadata.tsv +primaryKey Accession +colorSettingsUrl /gbdb/mm10/bbi/tad/organ_colors.json +subtrackUrls Accession=https://www.encodeproject.org/experiments/$$/ +maxCheckboxes 50 +html tadsEncode + + track tadsEncode_ENCSR005UON + parent tadsEncode on + shortLabel CH12.LX + longLabel ENCODE TADs in CH12.LX (ENCSR005UON) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/CH12LX.bb + color 6,218,147 + visibility dense + mouseOver Biosample: CH12.LX | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR097DFP + parent tadsEncode on + shortLabel Heart + longLabel ENCODE TADs in Heart (ENCSR097DFP) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/heart.bb + color 116,50,165 + visibility dense + mouseOver Biosample: Heart | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR639NRL + parent tadsEncode on + shortLabel Left cerebral cortex + longLabel ENCODE TADs in Left cerebral cortex (ENCSR639NRL) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/leftcerebralcortex.bb + color 155,155,18 + visibility dense + mouseOver Biosample: Left cerebral cortex | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR028GRK + parent tadsEncode on + shortLabel Mouse embryonic stem + longLabel ENCODE TADs in Mouse embryonic stem cell (ENCSR028GRK) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/mouseembryonicstemcell.bb + color 118,158,101 + visibility dense + mouseOver Biosample: Mouse embryonic stem cell | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR820CZQ + parent tadsEncode off + shortLabel Adrenal gland + longLabel ENCODE TADs in Adrenal gland (ENCSR820CZQ) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/adrenalgland.bb + color 90,179,68 + visibility dense + mouseOver Biosample: Adrenal gland | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR549VZT + parent tadsEncode off + shortLabel CH12F3 + longLabel ENCODE TADs in CH12F3 (ENCSR549VZT) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/CH12F3.bb + color 254,75,173 + visibility dense + mouseOver Biosample: CH12F3 | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR051JZL + parent tadsEncode off + shortLabel ES-E14 + longLabel ENCODE TADs in ES-E14 (ENCSR051JZL) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/ESE14.bb + color 118,158,101 + visibility dense + mouseOver Biosample: ES-E14 | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR136LVP + parent tadsEncode off + shortLabel Gastrocnemius + longLabel ENCODE TADs in Gastrocnemius (ENCSR136LVP) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/gastrocnemius.bb + color 137,135,170 + visibility dense + mouseOver Biosample: Gastrocnemius | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR471ZWB + parent tadsEncode off + shortLabel Mature B cell + longLabel ENCODE TADs in Mature B cell (ENCSR471ZWB) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/matureBcell.bb + color 254,75,173 + visibility dense + mouseOver Biosample: Mature B cell | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR357JYI + parent tadsEncode off + shortLabel Mouse trophoblast stem + longLabel ENCODE TADs in Mouse trophoblast stem cell (ENCSR357JYI) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/mousetrophoblaststemcell.bb + color 104,171,71 + visibility dense + mouseOver Biosample: Mouse trophoblast stem cell | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR080JTU + parent tadsEncode off + shortLabel Patski + longLabel ENCODE TADs in Patski (ENCSR080JTU) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/Patski.bb + color 92,161,153 + visibility dense + mouseOver Biosample: Patski | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR516LTA + parent tadsEncode off + shortLabel Regulatory T cell + longLabel ENCODE TADs in Regulatory T cell (ENCSR516LTA) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/regulatoryTcell.bb + color 254,75,173 + visibility dense + mouseOver Biosample: Regulatory T cell | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR858EVG + parent tadsEncode off + shortLabel T-helper 1 cell + longLabel ENCODE TADs in T-helper 1 cell (ENCSR858EVG) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/Thelper1cell.bb + color 254,75,173 + visibility dense + mouseOver Biosample: T-helper 1 cell | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR072ORZ + parent tadsEncode off + shortLabel T-helper 17 cell + longLabel ENCODE TADs in T-helper 17 cell (ENCSR072ORZ) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/Thelper17cell.bb + color 254,75,173 + visibility dense + mouseOver Biosample: T-helper 17 cell | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR407MXC + parent tadsEncode off + shortLabel T-helper 2 cell + longLabel ENCODE TADs in T-helper 2 cell (ENCSR407MXC) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/Thelper2cell.bb + color 254,75,173 + visibility dense + mouseOver Biosample: T-helper 2 cell | Arrowhead corner score: $cornerScore + + track tadsEncode_ENCSR799QDS + parent tadsEncode off + shortLabel v-Abl transformed + longLabel ENCODE TADs in v-Abl transformed pro-B cells (ENCSR799QDS) + type bigBed 4 + 5 + bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/vAbltransformedproBcells.bb + color 254,75,173 + visibility dense + mouseOver Biosample: v-Abl transformed pro-B cells | Arrowhead corner score: $cornerScore +