97c7de50efd34497c0e3f926f9afeaf9bbe45392 lrnassar Mon Sep 21 09:10:37 2026 -0700 Name the assay on every MaveMD map, and add ClinVar and gnomAD as related tracks. refs #37800 Two maps of the same gene routinely disagree, because they measured different things: PTEN abundance against PTEN lipid phosphatase activity, GCK activity against GCK abundance, KCNE1 trafficking with and without KCNQ1. Of the variants measured by more than one score set, 17% get opposite calls, and nothing on the map said why. The assay now travels with the map instead of sitting a click away on the details page. The legend above each matrix names the assay rather than repeating the same colour key on all 84 maps, and every cell mouseover ends with the same line. Method and model system come first because they are short and always present; the score set title is the part that truncates. The separator is a plain hyphen, since the legend is drawn as raster text and an HTML entity would appear literally there. relatedTracks.ra gains one-way links from mavemd to clinvar and gnomadVariants. MaveMD ships a ClinVar and gnomAD snapshot taken from the MaveDB API, and its calibrations were computed against that snapshot, so the imported values stay; the links point readers at our always-current tracks. One-way because MaveMD is too narrow to earn a line on two of the most heavily used tracks we have. diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index 451f1cb37c5..b26a54f52f0 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -353,30 +353,36 @@ 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 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 hg19 geneHancer vistaEnhancersBb Enhancers tested for activity in transgenic mouse embryos hg19 vistaEnhancersBb geneHancer Predicted enhancers and promoters with their likely target genes hg19 cpgIslandSuper dnaMethylation Measured methylation levels, which are often depleted over these islands hg19 dnaMethylation cpgIslandSuper CpG-dense regions predicted from the reference sequence hg19 epdNew fantom5 Transcription start sites and their usage, measured by CAGE hg19 fantom5 epdNew Experimentally supported promoters curated in EPDnew mm39 cpgIslandSuper dnaMethylation Measured methylation levels, which are often depleted over these islands mm39 dnaMethylation cpgIslandSuper CpG-dense regions predicted from the reference sequence mm10 cCREs refSeqFuncElems Regulatory and other functional elements curated by NCBI from the literature mm10 refSeqFuncElems cCREs Candidate regulatory elements called from ENCODE chromatin data @@ -602,30 +608,35 @@ hg38 spliceAIWt spliceAI The same model scored for variants, rather than for the reference sequence hg38 abSplice spliceVarDb Splicing variants with experimental validation, useful for checking these predictions hg38 spliceVarDb abSplice Predicted aberrant splicing, scored per variant and tissue hg38 spliceImpactSuper predictionScoresSuper Pathogenicity scores for coding and non-coding variants generally, not only splicing hg38 predictionScoresSuper spliceImpactSuper Prediction scores and databases for variants that disrupt splicing hg38 nmd spliceImpactSuper Predicted and validated splice-altering variants, a common source of premature termination codons hg38 spliceImpactSuper nmd Regions where premature termination codons are predicted to escape nonsense-mediated decay hg19 ~spliceAI abSplice Another deep-learning predictor of splice-altering variants hg19 spliceImpactSuper predictionScoresSuper Pathogenicity scores for coding and non-coding variants generally, not only splicing hg19 predictionScoresSuper spliceImpactSuper Prediction scores and databases for variants that disrupt splicing # MaveDB / MaveMD cross-links: hg38 mavedb mavemd The clinically curated subset, with ACMG functional evidence calibrations hg38 mavemd mavedb The full set of variant effect maps in MaveDB, without clinical calibration +# One-way: MaveMD carries a snapshot of ClinVar and gnomAD annotations from the MaveDB API, +# so point readers at our always-current tracks. No reciprocal line, since MaveMD is too +# narrow to be worth listing on two of the most heavily used tracks we have. +hg38 >mavemd clinvar Our current ClinVar release, rather than the snapshot MaveMD's calibrations were computed against +hg38 >mavemd gnomadVariants Our current gnomAD release, rather than the frequencies MaveMD supplies with each measurement # Constraint score cross-links: hg38 constraintSuper predictionScoresSuper Per-variant deleteriousness and pathogenicity scores, rather than regional constraint hg38 predictionScoresSuper constraintSuper Regional and gene-level constraint measured from population variation hg38 ~jarvis ukbDepletion Another score for how depleted of variation a non-coding region is hg38 ~hmc gnomadPLI Another constraint metric derived from the absence of variation in population data hg38 hmc ucscGenePfam The Pfam protein domains that homologous missense constraint is calculated over hg38 ucscGenePfam hmc Missense constraint measured across homologous positions within these domains hg38 promoterAi jarvis A score prioritizing non-coding regions more broadly, not only promoters hg38 jarvis promoterAi A deep-learning predictor for variants in promoter regions specifically hg19 constraintSuper predictionScoresSuper Per-variant deleteriousness and pathogenicity scores, rather than regional constraint hg19 predictionScoresSuper constraintSuper Regional and gene-level constraint measured from population variation hg19 ~jarvis ukbDepletion Another score for how depleted of variation a non-coding region is hg19 ~hmc gnomadPLI Another constraint metric derived from the absence of variation in population data