1aca3edb987bc90a17be6a22efad5446d4e42029 jnavarr5 Fri Sep 25 13:44:48 2026 -0700 Updating the packmode labels to show the episignature instead of the CpG ID. Adding semicolons to the filters so it matches the MethaDory track, refs #38371 diff --git src/hg/makeDb/trackDb/human/hg38/episignatures.ra src/hg/makeDb/trackDb/human/hg38/episignatures.ra index cca3090e4e5..d31cd18ba31 100644 --- src/hg/makeDb/trackDb/human/hg38/episignatures.ra +++ src/hg/makeDb/trackDb/human/hg38/episignatures.ra @@ -1,93 +1,95 @@ track episignatures superTrack on shortLabel Episignatures longLabel DNA methylation episignatures of rare developmental disorders group regulation html episignatures.html # Supertrack-level filter. Rendered on the supertrack's own hgTrackUi page # (superTrackUi() in hgTrackUi.c). Cart values stored under # "episignatures.filter.maxAbsDelta.min/max" are inherited at read time by # both subtracks via cartOptionalStringClosestToHome() walking tdb->parent, # so one control filters methaDory and epigenCentral together. A # subtrack-level filter.maxAbsDelta would always win over this one; neither # subtrack sets one, since the field means the same thing (and is named the # same, maxAbsDelta, in both .as files) in both. filterByRange.maxAbsDelta on filter.maxAbsDelta 0:1 filterLimits.maxAbsDelta 0:1 filterLabel.maxAbsDelta Absolute delta-beta of the strongest episignature at this probe track methaDory parent episignatures shortLabel MethaDory longLabel MethaDory: CpG probes of published DNA methylation episignatures type bigBed 9 + bigDataUrl /gbdb/hg38/episignatures/methaDory.bb visibility pack itemRgb on noScoreFilter on maxWindowCoverage 10000000 searchIndex name skipFields disorders,signatures,loci,deltaBetas,pvalues,studies,disorderSummary detailsDynamicTable _jsonSignatures|Episignatures at this CpG site urls publications="https://pubmed.ncbi.nlm.nih.gov/$$/" mouseOver <b>Probe:</b> ${name}<br><b>Episignatures at this probe:</b> ${sigCount}<br><b>Disorders:</b> ${disorderSummary}<br><b>Direction and strength:</b> ${direction}<br><b>Largest absolute delta-beta:</b> ${maxAbsDelta} filterValues.disorders 16p11.2 microdeletion,ARID1A duplication syndrome,ARID1A-ARID1B.c.6200,ARID1B duplication syndrome,Alpha-thalassemia X-linked intellectual disability,Arboleda-Tham syndrome,Armfield X-linked intellectual disability,Au-Kline syndrome,Autosomal dominant intellectual developmental disorder 65,BCL11B-related disorder,BRWD3-related genetic disorder (MRX93),Bafopathies,Beck-Fahrner syndrome,Bohring-Opitz Syndrome,Börjeson-Forssman-Lehmann syndrome,CDK13-Related Congenital Heart Defects; Dysmorphic Facial Features; and Intellectual Developmental Disorder,CHARGE syndrome,CHD2-related neurodevelopmental disorder,CHD8-related neurodevelopmental disorder with overgrowth,CTCF-related disorder,CUL3-related neurodevelopmental disorder,Chung-Jansen syndrome,Claes-Jensen syndrome,Coffin-Siris Syndrome 3,Coffin-Siris syndrome 1,Coffin-Siris syndrome 6,Coffin-Siris syndrome 9,Cornelia de Lange syndrome,DEGCAGS syndrome,DNMT1-related disorder,DYRK1A syndrome,DiGeorge syndrome or velocardiofacial syndrome,Down syndrome,Dup7,EHMT1-duplication,Fanconi anemia,Fetal alcohol syndrome,Floating harbour syndrome,Gabriele-de Vries syndrome,Genitopatellar syndrome,HIST1H1E syndrome,HNRNPU-related neurodevelopmental disorder,Hao-Fountain syndrome,Helsmoortel-Van der Aa syndrome (central variants),Helsmoortel-Van der Aa syndrome (terminal variants),ICF syndrome,ICF2; ICF3; ICF4,Intellectual developmental disorder; X-linked 97,Intellectual developmental disorder; X-linked syndromic; Nascimento type,Intellectual developmental disorder; autosomal dominant 49,JARID2-related syndrome,KBG syndrome,KDM2A syndrome,KDM2B-related neurodevelopmental disorder,KMT2B dystonia syndrome,KMT2C-related syndrome,KMT5B syndrome,Kabuki syndrome,Karayol-Borroto-Haghshenas neurodevelopmental syndrome,Kleefstra syndrome,Koolen-de Vries syndrome,Luscan-Lumish syndrome,MN1 C-terminal truncation (MCTT) syndrome,MORC2-related disorders,Menke-Hennekam syndrome,Mowat-Wilson syndrome,Myopathy; lactic acidosis; and sideroblastic anemia 2,NOTCH1 Congenital heart defects,NSD1 duplication,Neurodevelopmental disorder with dysmorphic facies and behavioral abnormalities,Neurodevelopmental disorder with impaired speech and hyperkinetic movements,Nicolaides-Baraitser syndrome,Nil-Deshwar Neurodevelopmental Syndrome,PURA-related disorder,Phelan-McDermid syndrome,Pitt-Hopkins syndrome,Potocki-Lupski syndrome,Prenatal valproic acid exposure,RNU2-2,RNU2-2.biallelic,RNU2-2.n35,RNU4-2,Recurrent constellations of embryonic malformations,Renpenning syndrome,Rubinstein-Taybi Syndrome,SETD1B-related neurodevelopmental disorder,SETD2c1740,SETD5-related disorder,SMARCA4c2650,SPEN haploinsufficiency,SRCAP.proximal,Say-Barber-Biesecker-Young-Simpson syndrome,Schuurs-Hoeijmakers syndrome,Sifrim-Hitz-Weiss syndrome,Skeletal Dysplasia; Tooth Anomalies; and Developmental Delay,Smith-Magenis Syndrome,Smith-Magenis syndrome,Snijders Blok-Campeau syndrome,Sotos syndrome,Tatton-Brown-Rahman syndrome,Weaver syndrome,Wiedemann-Steiner syndrome,Witteveen-Kolk syndrome,Wolf-Hirschhorn syndrome,intellectual disability and blepharophimosis filterType.disorders multipleListOr filterValues.loci ADNPc,ADNPt,ANKRD11-chr16q24.3del,ARID1A-ARID1B-SMARCB1-SMARCA4-SMARCA2,ARID1A-ARID1B.c.6200,ARID1Adup,ARID1B,ARID1Bdup,ARID2,ASXL1,ATRX,BCL11B,BRWD3,CDCA7-ZBTB24-HELLS,CDK13,CHD2,CHD3,CHD4,CHD7,CHD8,CREBBP-EP300,CREBBP-EP300.MKHK,CREBBP.RSTS1,CTCF,CUL3,DNMT1,DNMT3A,DNMT3B,DOT1L,DYRK1A,EED-EZH2,EHMT1,EHMT1dup,EP300.RSTS2,EZH2,FAM50A,FANCA,FASD,HIST1H1E,HNRNPK,HNRNPU,JARID2,KANSL1,KAT6A,KAT6B.GTPTS,KAT6B.SBBYSS,KDM2A,KDM2B,KDM4B,KDM5C,KMT2A,KMT2Bdyt,KMT2C,KMT2D,KMT2D-KDM6A,KMT5B,MN1,MORC2,MSL2,NIPBL-RAD21-SMC3-SMC1A,NOTCH1,NSD1,NSD1dup,NSD2,PACS1,PHF6,PHIP1,PQBP1,PTBP1,PURA,RNU2-2,RNU2-2.biallellic,RNU2-2.n35,RNU4-2,SETD1B,SETD2.LLS,SETD2c1740,SETD5,SIN3A,SMARCA2,SMARCA2.BISS,SMARCA2bis-ADNPbnl,SMARCA4c2650,SMARCB1,SMS,SOX11,SPEN,SRCAP.FLHS,SRCAP.proximal,SRSF1,TCF4,TET3,TRIP12,UBE2A,USP7,VACTERL.combined,VACTERL.intermediate,VACTERL.robust,ValproicAcid,YARS2,YY1,ZEB2,ZNF142,ZNF699,ZNF711,chr16p11.2del,chr17p11.2del,chr17p11.2dup,chr21tris,chr22q11.2del,chr22q13.3del,chr7q11.23del,chr7q11.23dup filterType.loci multipleListOr filterValues.studies AlJawahiri2022,Anderson2026,ArefEshghi2018,ArefEshghi2020,Awamleh2022,Awamleh2023,Awamleh2024,Bacalini2015,Bend2019,Bogaert2023,Breen2020,Butcher2017,Cappuccio2020,Caraffi2023,ChaterDiehl2019,Choufani2015,Choufani2020,Choufani2022,Ciolfi2020,Ciolfi2021,Cobben2018,CoenenvanderSpek2023,Courraud2021,Dombrowsky2026,Foroutan2022,Goodman2020,Grafodatskaya2013,Haghshenas2021,Haghshenas2023,Haghshenas2024,Hildonen2025,Houdayer2025,Jeffries2019,Karayol2024,Karimi2024,Kawai2024,Kimura2020,Krzyzewska2019,Krzyzewska2023,LaFlamme2024,Lee2023,Leitao2025,Levy2022,Mak2025,Masson2025,Naumova2021,Nava2025,Nil2023,Pagliara2023,Peymani2026,Radio2021,Rooney2021,Rooney2023,Rots2021,Rots2024,Rouxel2022,Sabbagh2024,Sabbagh2026,Santini2025,Sarli2024,Schenkel2018,Schenkel2021,Siu2017,Strong2015,Velasco2021,Verberne2022,Vos2024,Wang2026,Xiao2024,vanderLaan2022,vanderLaan2023,vanderLaan2024,vanderLaan2025,vanderSluijs2024 filterType.studies multipleListOr filterLabel.disorders Disorder filterLabel.loci Gene or locus filterLabel.studies Study filterValues.direction Strong hypermethylation,Weak hypermethylation,Weak hypomethylation,Strong hypomethylation,Conflicting filterType.direction multipleListOr filterLabel.direction Direction and strength track epigenCentral parent episignatures shortLabel EpigenCentral longLabel EpigenCentral: CpG probes of curated DNA methylation episignatures type bigBed 9 + bigDataUrl /gbdb/hg38/episignatures/epigenCentral.bb visibility pack itemRgb on noScoreFilter on tableBrowser off maxWindowCoverage 10000000 searchIndex name + labelFields name,displaySignature + defaultLabelFields displaySignature skipFields signatureList detailsDynamicTable comparisonTable|Episignatures at this CpG site urls displayOmim="https://omim.org/entry/$$" mouseOver <b>Probe:</b> ${name}<br><b>Episignatures at this probe:</b> ${sigCount}<br><b>Strongest episignature:</b> ${displaySignature}<br><b>Disorder:</b> ${displayDisorder}<br><b>OMIM:</b> ${displayOmim}<br><b>Direction:</b> ${direction}<br><b>Absolute delta-beta:</b> ${maxAbsDelta} filterByRange.sigCount on filter.sigCount 1:6 filterLimits.sigCount 1:6 filterLabel.sigCount Number of episignatures at this probe filterValues.direction Gain,Loss filterType.direction multipleListOr filterLabel.direction Direction of methylation change - filterValues.signatureList 16pDel|Autism spectrum (16pDel),ANKRD11|KBG syndrome (ANKRD11),ARID1B|Coffin-Siris syndrome 1 (ARID1B),ASXL1|Bohring-Opitz syndrome (ASXL1),CHD7|CHARGE syndrome (CHD7),CHD8|Intellectual developmental disorder with autism and macrocephaly (CHD8),Dup7|Chromosome 7q11.23 duplication syndrome (Dup7),DYRK1A|Intellectual developmental disorder autosomal dominant 7 (DYRK1A),EHMT1|Kleefstra syndrome 1 (EHMT1),EZH2|Weaver syndrome (EZH2),FHS|Floating-Harbor syndrome (FHS),HNRNPK|Au-Kline syndrome (HNRNPK),KANSL1|Koolen-De Vries syndrome (KANSL1),KMT2A|Wiedemann-Steiner syndrome (KMT2A),KMT2B|Dystonia 28 childhood-onset (KMT2B),KMT2C|Kleefstra syndrome 2 (KMT2C),KMT2D_2017|Kabuki syndrome 1 (KMT2D_2017),KMT2D_2026|Kabuki syndrome 1 (KMT2D_2026),MN1|CEBALID syndrome (MN1),NSD1|Sotos syndrome (NSD1),SMARCA2|Nicolaides-Baraitser syndrome (SMARCA2),SRCAP|Developmental delay hypotonia musculoskeletal defects and behavioral abnormalities (SRCAP),T21|Down syndrome (T21),Williams|Williams-Beuren syndrome (Williams) + filterValues.signatureList 16pDel|Autism spectrum (16pDel),ANKRD11|KBG syndrome (ANKRD11),ARID1B|Coffin-Siris syndrome 1 (ARID1B),ASXL1|Bohring-Opitz syndrome (ASXL1),CHD7|CHARGE syndrome (CHD7),CHD8|Intellectual developmental disorder with autism and macrocephaly (CHD8),Dup7|Chromosome 7q11.23 duplication syndrome (Dup7),DYRK1A|Intellectual developmental disorder; autosomal dominant 7 (DYRK1A),EHMT1|Kleefstra syndrome 1 (EHMT1),EZH2|Weaver syndrome (EZH2),FHS|Floating-Harbor syndrome (FHS),HNRNPK|Au-Kline syndrome (HNRNPK),KANSL1|Koolen-De Vries syndrome (KANSL1),KMT2A|Wiedemann-Steiner syndrome (KMT2A),KMT2B|Dystonia 28; childhood-onset (KMT2B),KMT2C|Kleefstra syndrome 2 (KMT2C),KMT2D_2017|Kabuki syndrome 1 (KMT2D_2017),KMT2D_2026|Kabuki syndrome 1 (KMT2D_2026),MN1|CEBALID syndrome (MN1),NSD1|Sotos syndrome (NSD1),SMARCA2|Nicolaides-Baraitser syndrome (SMARCA2),SRCAP|Developmental delay; hypotonia; musculoskeletal defects; and behavioral abnormalities (SRCAP),T21|Down syndrome (T21),Williams|Williams-Beuren syndrome (Williams) filterType.signatureList multipleListAnd filterLabel.signatureList Episignature searchTable epigenCentral searchMethod exact # see the methaDory spec below for why termRegex and semiShortCircuit are needed searchType bigBed termRegex ^cg[0-9]+$ semiShortCircuit 1 searchDescription Illumina methylation array probe of an EpigenCentral episignature searchPriority 51 searchTable methaDory searchMethod exact # termRegex puts this spec on the short-circuiting list, the only one that runs # when another short spec already matched; semiShortCircuit then keeps the # Illumina array specs (priority 55) running as well, so a probe ID finds both searchType bigBed termRegex ^(cg[0-9]+|ch\.[0-9XYM]+\.[0-9]+[FR])$ semiShortCircuit 1 searchDescription Illumina methylation array probe of a published episignature searchPriority 50