f3020b17f2fcd376aca99d97d778c11625c0927f jnavarr5 Fri Sep 25 17:49:08 2026 -0700 Relating different TSS and promoter tracks, refs #35528 diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index 4eacfd8c47a..306dfdbd6aa 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -347,30 +347,34 @@ hg38 >tgpArchive varFreqs Allele frequencies from many newer population-scale sequencing projects # Regulation cross-links: hg38 geneHancer oreganno Literature-curated regulatory elements and transcription factor binding sites hg38 oreganno geneHancer Enhancers and promoters with predicted target genes, integrated from several sources hg38 geneHancer vistaEnhancersBb Enhancers tested for activity in transgenic mouse embryos hg38 vistaEnhancersBb geneHancer Predicted enhancers and promoters with their likely target genes hg38 cCREs refSeqFuncElems Regulatory and other functional elements curated by NCBI from the literature hg38 refSeqFuncElems cCREs Candidate regulatory elements called from ENCODE chromatin data hg38 tads hicAndMicroC The Hi-C and Micro-C contact maps that domain boundaries are called from hg38 hicAndMicroC tads Topologically associating domains and boundaries called from contact maps hg38 cpgIslandSuper dnaMethylation Measured methylation levels, which are often depleted over these islands hg38 dnaMethylation cpgIslandSuper CpG-dense regions predicted from the reference sequence hg38 epdNew fantom5 Transcription start sites and their usage, measured by CAGE hg38 fantom5 epdNew Experimentally supported promoters curated in EPDnew +hg38 transcriptionStart fantom5 Transcription start sites and their usage, measured by CAGE +hg38 fantom5 transcriptionStart Transcription initiation measured by PRO-cap and predicted by ProCapNet +hg38 transcriptionStart epdNew Experimentally supported promoters curated in EPDnew +hg38 epdNew transcriptionStart Transcription initiation measured by PRO-cap and predicted by ProCapNet hg38 gtexEqtlHighConf gtexGeneV8 Gene expression levels in the same GTEx tissues hg38 gtexGeneV8 gtexEqtlHighConf Variants associated with expression of nearby genes in the same tissues hg38 jaspar wgEncodeReg4TfPeaks Transcription factor peak clusters from ENCODE 4 ChIP-seq experiments hg38 wgEncodeReg4TfPeaks jaspar Computationally predicted binding sites from position weight matrices hg38 singleCellSignalsPeaks wgEncodeReg4Atac Bulk ATAC-seq accessibility, averaged by organ and tissue hg38 wgEncodeReg4Atac singleCellSignalsPeaks Chromatin accessibility resolved by individual cell type hg38 fiberSeq dnaMethylation Methylation measured by bisulfite and other assays hg38 dnaMethylation fiberSeq Accessibility and CpG methylation read from the same single molecules hg38 fiberSeq cCREs Candidate regulatory elements called from short-read ENCODE data hg38 cCREs fiberSeq Regulatory elements called on single molecules, resolved by haplotype hg38 fiberSeq wgEncodeRegDnase Chromatin accessibility measured by DNase hypersensitivity hg38 wgEncodeRegDnase fiberSeq Chromatin accessibility measured one molecule at a time hg19 geneHancer oreganno Literature-curated regulatory elements and transcription factor binding sites hg19 oreganno geneHancer Enhancers and promoters with predicted target genes, integrated from several sources