8c31969cb13f9887a76480767e68c0b5421e2a65 dschmelt Tue May 26 13:43:43 2020 -0700 Updating html and pennantIcon #25130 diff --git src/hg/makeDb/trackDb/human/trackDb.gtex.ra src/hg/makeDb/trackDb/human/trackDb.gtex.ra index dd8da6d..bd6f3f3 100644 --- src/hg/makeDb/trackDb/human/trackDb.gtex.ra +++ src/hg/makeDb/trackDb/human/trackDb.gtex.ra @@ -1,591 +1,591 @@ # GTEx (Genotype Tissue Expression) project tracks # Allele-specific expression include trackDb.gtexAwgAse.ra # Gene expression track gtexGene shortLabel GTEx Gene longLabel Gene Expression in 53 tissues from GTEx RNA-seq of 8555 samples (570 donors) type bed 6 + html gtexGeneExpr group expression priority 1 maxItems 200 spectrum on visibility pack searchTable gtexGene query select chrom, chromStart, chromEnd, geneId from %s where geneId like '%s%%' termRegex gtex:ENSG[0-9]+(\.[0-9]+)? termPrefix gtex: shortCircuit 1 track gtexTranscExpr shortLabel GTEx Transcript longLabel Transcript Expression in 53 tissues from GTEx RNA-seq of 8555 samples/570 donors type bigBarChart barChartLabel Tissue types barChartUnit TPM # Get the barChartLabels from the last line in the bed file. barChartBars \ Adipose-Subcutaneous Adipose-Visceral_(Omentum) Adrenal_Gland Artery-Aorta \ Artery-Coronary Artery-Tibial Bladder Brain-Amygdala Brain-Anterior_cingulate_cortex_(BA24) \ Brain-Caudate_(basal_ganglia) Brain-Cerebellar_Hemisphere Brain-Cerebellum Brain-Cortex \ Brain-Frontal_Cortex_(BA9) Brain-Hippocampus Brain-Hypothalamus \ Brain-Nucleus_accumbens_(basal_ganglia) Brain-Putamen_(basal_ganglia) \ Brain-Spinal_cord_(cervical_c-1) Brain-Substantia_nigra Breast-Mammary_Tissue \ Cells-EBV-transformed_lymphocytes Cells-Transformed_fibroblasts Cervix-Ectocervix \ Cervix-Endocervix Colon-Sigmoid Colon-Transverse Esophagus-Gastroesophageal_Junction \ Esophagus-Mucosa Esophagus-Muscularis Fallopian_Tube Heart-Atrial_Appendage \ Heart-Left_Ventricle Kidney-Cortex Liver Lung Minor_Salivary_Gland Muscle-Skeletal \ Nerve-Tibial Ovary Pancreas Pituitary Prostate Skin-Not_Sun_Exposed_(Suprapubic) \ Skin-Sun_Exposed_(Lower_leg) Small_Intestine-Terminal_Ileum Spleen Stomach Testis \ Thyroid Uterus Vagina Whole_Blood barChartColors \ \#FFA54F #EE9A00 #8FBC8F #8B1C62 #EE6A50 #FF0000 #CDB79E #EEEE00 \ \#EEEE00 #EEEE00 #EEEE00 #EEEE00 #EEEE00 #EEEE00 #EEEE00 #EEEE00 \ \#EEEE00 #EEEE00 #EEEE00 #EEEE00 #00CDCD #EE82EE #9AC0CD #EED5D2 \ \#EED5D2 #CDB79E #EEC591 #8B7355 #8B7355 #CDAA7D #EED5D2 #B452CD \ \#7A378B #CDB79E #CDB79E #9ACD32 #CDB79E #7A67EE #FFD700 #FFB6C1 \ \#CD9B1D #B4EEB4 #D9D9D9 #3A5FCD #1E90FF #CDB79E #CDB79E #FFD39B \ \#A6A6A6 #008B45 #EED5D2 #EED5D2 #FF00FF barChartMatrixUrl /gbdb/hgFixed/human/expMatrix/cleanGtexMatrix.tab barChartSampleUrl /gbdb/hgFixed/human/expMatrix/cleanGtexSamples.tab barChartMetric median maxLimit 8000 maxItems 300 defaultLabelFields name2, name labelFields name2, name group expression priority 1.1 # Older, in progress, and experimental track gtexGeneV4 release alpha type bed 6 + shortLabel GTEx Expr V4 longLabel Gene Expression in 53 tissues from GTEx RNA-seq of 2921 samples, 209 donors (V4, Aug 2014) html gtexGeneExprV4 group expression priority 10.1 track gtexGeneV8 shortLabel GTEx Gene V8 longLabel Gene Expression in 54 tissues from GTEx RNA-seq of 17382 samples, 948 donors (V8, Aug 2019) type bed 6 + -pennantIcon new red ../goldenPath/newsarch.html#052220a "Note: Released May. 22, 2020" +pennantIcon new red ../goldenPath/newsarch.html#052220a "Released May. 22, 2020" group expression maxItems 200 spectrum on priority 10.1 track gtexSnp release alpha type bed 4 shortLabel GTEx Variant longLabel Genetic variants imputed from genotyping of GTEx samples (209 donors) group expression html getxEqtlSnp priority 10.15 track gtexEqtlSnp release alpha type bed 4 shortLabel GTEx Pilot eQTL longLabel Genetic variants identified by GTEx V4 (pilot) analysis as significantly affecting gene expression group expression priority 10.16 track gtexExon compositeTrack on shortLabel GTEx Exon longLabel Exon Expression in 53 tissues from GTEx RNA-seq of 2921 samples (209 donors) dragAndDrop subTracks group expression priority 10.2 type bed 6 exonArrows off minGrayLevel 2 darkerLabels on subGroup1 tissue Tissue \ adiposeSubcut=adiposeSubcut \ adiposeVisceral=adiposeVisceral \ adrenalGland=adrenalGland \ arteryAorta=arteryAorta \ arteryCoronary=arteryCoronary \ arteryTibial=arteryTibial \ bladder=bladder \ brainAmygdala=brainAmygdala \ brainAnCinCortex=brainAnCinCortex \ brainCaudate=brainCaudate \ brainCerebelHemi=brainCerebelHemi \ brainCerebellum=brainCerebellum \ brainCortex=brainCortex \ brainFrontCortex=brainFrontCortex \ brainHippocampus=brainHippocampus \ brainHypothalamus=brainHypothalamus \ brainNucAccumbens=brainNucAccumbens \ brainPutamen=brainPutamen \ brainSpinalcord=brainSpinalcord \ brainSubstanNigra=brainSubstanNigra \ breastMamTissue=breastMamTissue \ xformedlymphocytes=xformedlymphocytes \ xformedfibroblasts=xformedfibroblasts \ ectocervix=ectocervix \ endocervix=endocervix \ colonSigmoid=colonSigmoid \ colonTransverse=colonTransverse \ esophagusJunction=esophagusJunction \ esophagusMucosa=esophagusMucosa \ esophagusMuscular=esophagusMuscular \ fallopianTube=fallopianTube \ heartAtrialAppend=heartAtrialAppend \ heartLeftVentricl=heartLeftVentricl \ kidneyCortex=kidneyCortex \ liver=liver \ lung=lung \ minorSalivGland=minorSalivGland \ muscleSkeletal=muscleSkeletal \ nerveTibial=nerveTibial \ ovary=ovary \ pancreas=pancreas \ pituitary=pituitary \ prostate=prostate \ skinNotExposed=skinNotExposed \ skinExposed=skinExposed \ smallIntestine=smallIntestine \ spleen=spleen \ stomach=stomach \ testis=testis \ thyroid=thyroid \ uterus=uterus \ vagina=vagina \ wholeBlood=wholeBlood track gtexTissueExonMedianAdiposeSubcut parent gtexExon shortLabel adiposeSubcut longLabel Exon Expression in Adipose - Subcutaneous from GTEx RNA-seq of 128 samples subGroups tissue=adiposeSubcut color 255,165,79 spectrum on track gtexTissueExonMedianAdiposeVisceral parent gtexExon shortLabel adiposeVisceral longLabel Exon Expression in Adipose - Visceral (Omentum) from GTEx RNA-seq of 31 samples subGroups tissue=adiposeVisceral color 238,154,0 spectrum on track gtexTissueExonMedianAdrenalGland parent gtexExon shortLabel adrenalGland longLabel Exon Expression in Adrenal Gland from GTEx RNA-seq of 52 samples subGroups tissue=adrenalGland color 116,215,116 spectrum on track gtexTissueExonMedianArteryAorta parent gtexExon shortLabel arteryAorta longLabel Exon Expression in Artery - Aorta from GTEx RNA-seq of 82 samples subGroups tissue=arteryAorta color 164,3,104 spectrum on track gtexTissueExonMedianArteryCoronary parent gtexExon shortLabel arteryCoronary longLabel Exon Expression in Artery - Coronary from GTEx RNA-seq of 44 samples subGroups tissue=arteryCoronary color 255,95,63 spectrum on track gtexTissueExonMedianArteryTibial parent gtexExon shortLabel arteryTibial longLabel Exon Expression in Artery - Tibial from GTEx RNA-seq of 137 samples subGroups tissue=arteryTibial color 255,0,0 spectrum on track gtexTissueExonMedianBladder parent gtexExon shortLabel bladder longLabel Exon Expression in Bladder from GTEx RNA-seq of 11 samples subGroups tissue=bladder color 227,184,136 spectrum on track gtexTissueExonMedianBrainAmygdala parent gtexExon shortLabel brainAmygdala longLabel Exon Expression in Brain - Amygdala from GTEx RNA-seq of 26 samples subGroups tissue=brainAmygdala color 238,238,0 spectrum on track gtexTissueExonMedianBrainAnCinCortex parent gtexExon shortLabel brainAnCinCortex longLabel Exon Expression in Brain - Anterior cingulate cortex (BA24) from GTEx RNA-seq of 22 samples subGroups tissue=brainAnCinCortex color 238,238,0 spectrum on track gtexTissueExonMedianBrainCaudate parent gtexExon shortLabel brainCaudate longLabel Exon Expression in Brain - Caudate (basal ganglia) from GTEx RNA-seq of 36 samples subGroups tissue=brainCaudate color 238,238,0 spectrum on track gtexTissueExonMedianBrainCerebelHemi parent gtexExon shortLabel brainCerebelHemi longLabel Exon Expression in Brain - Cerebellar Hemisphere from GTEx RNA-seq of 29 samples subGroups tissue=brainCerebelHemi color 238,238,0 spectrum on track gtexTissueExonMedianBrainCerebellum parent gtexExon shortLabel brainCerebellum longLabel Exon Expression in Brain - Cerebellum from GTEx RNA-seq of 31 samples subGroups tissue=brainCerebellum color 238,238,0 spectrum on track gtexTissueExonMedianBrainCortex parent gtexExon shortLabel brainCortex longLabel Exon Expression in Brain - Cortex from GTEx RNA-seq of 25 samples subGroups tissue=brainCortex color 238,238,0 spectrum on track gtexTissueExonMedianBrainFrontCortex parent gtexExon shortLabel brainFrontCortex longLabel Exon Expression in Brain - Frontal Cortex (BA9) from GTEx RNA-seq of 28 samples subGroups tissue=brainFrontCortex color 238,238,0 spectrum on track gtexTissueExonMedianBrainHippocampus parent gtexExon shortLabel brainHippocampus longLabel Exon Expression in Brain - Hippocampus from GTEx RNA-seq of 28 samples subGroups tissue=brainHippocampus color 238,238,0 spectrum on track gtexTissueExonMedianBrainHypothalamus parent gtexExon shortLabel brainHypothalamus longLabel Exon Expression in Brain - Hypothalamus from GTEx RNA-seq of 30 samples subGroups tissue=brainHypothalamus color 238,238,0 spectrum on track gtexTissueExonMedianBrainNucAccumbens parent gtexExon shortLabel brainNucAccumbens longLabel Exon Expression in Brain - Nucleus accumbens (basal ganglia) from GTEx RNA-seq of 32 samples subGroups tissue=brainNucAccumbens color 238,238,0 spectrum on track gtexTissueExonMedianBrainPutamen parent gtexExon shortLabel brainPutamen longLabel Exon Expression in Brain - Putamen (basal ganglia) from GTEx RNA-seq of 24 samples subGroups tissue=brainPutamen color 238,238,0 spectrum on track gtexTissueExonMedianBrainSpinalcord parent gtexExon shortLabel brainSpinalcord longLabel Exon Expression in Brain - Spinal cord (cervical c-1) from GTEx RNA-seq of 19 samples subGroups tissue=brainSpinalcord color 238,238,0 spectrum on track gtexTissueExonMedianBrainSubstanNigra parent gtexExon shortLabel brainSubstanNigra longLabel Exon Expression in Brain - Substantia nigra from GTEx RNA-seq of 27 samples subGroups tissue=brainSubstanNigra color 238,238,0 spectrum on track gtexTissueExonMedianBreastMamTissue parent gtexExon shortLabel breastMamTissue longLabel Exon Expression in Breast - Mammary Tissue from GTEx RNA-seq of 66 samples subGroups tissue=breastMamTissue color 0,205,205 spectrum on track gtexTissueExonMedianXformedlymphocytes parent gtexExon shortLabel xformedlymphocytes longLabel Exon Expression in Cells - EBV-transformed lymphocytes from GTEx RNA-seq of 54 samples subGroups tissue=xformedlymphocytes color 255,113,255 spectrum on track gtexTissueExonMedianXformedfibroblasts parent gtexExon shortLabel xformedfibroblasts longLabel Exon Expression in Cells - Transformed fibroblasts from GTEx RNA-seq of 155 samples subGroups tissue=xformedfibroblasts color 131,203,228 spectrum on track gtexTissueExonMedianEctocervix parent gtexExon shortLabel ectocervix longLabel Exon Expression in Cervix - Ectocervix from GTEx RNA-seq of 6 samples subGroups tissue=ectocervix color 247,205,200 spectrum on track gtexTissueExonMedianEndocervix parent gtexExon shortLabel endocervix longLabel Exon Expression in Cervix - Endocervix from GTEx RNA-seq of 3 samples subGroups tissue=endocervix color 247,205,200 spectrum on track gtexTissueExonMedianColonSigmoid parent gtexExon shortLabel colonSigmoid longLabel Exon Expression in Colon - Sigmoid from GTEx RNA-seq of 13 samples subGroups tissue=colonSigmoid color 227,184,136 spectrum on track gtexTissueExonMedianColonTransverse parent gtexExon shortLabel colonTransverse longLabel Exon Expression in Colon - Transverse from GTEx RNA-seq of 61 samples subGroups tissue=colonTransverse color 255,199,128 spectrum on track gtexTissueExonMedianEsophagusJunction parent gtexExon shortLabel esophagusJunction longLabel Exon Expression in Esophagus - Gastroesophageal Junction from GTEx RNA-seq of 22 samples subGroups tissue=esophagusJunction color 172,119,52 spectrum on track gtexTissueExonMedianEsophagusMucosa parent gtexExon shortLabel esophagusMucosa longLabel Exon Expression in Esophagus - Mucosa from GTEx RNA-seq of 106 samples subGroups tissue=esophagusMucosa color 172,119,52 spectrum on track gtexTissueExonMedianEsophagusMuscular parent gtexExon shortLabel esophagusMuscular longLabel Exon Expression in Esophagus - Muscularis from GTEx RNA-seq of 99 samples subGroups tissue=esophagusMuscular color 232,173,98 spectrum on track gtexTissueExonMedianFallopianTube parent gtexExon shortLabel fallopianTube longLabel Exon Expression in Fallopian Tube from GTEx RNA-seq of 6 samples subGroups tissue=fallopianTube color 247,205,200 spectrum on track gtexTissueExonMedianHeartAtrialAppend parent gtexExon shortLabel heartAtrialAppend longLabel Exon Expression in Heart - Atrial Appendage from GTEx RNA-seq of 38 samples subGroups tissue=heartAtrialAppend color 200,49,238 spectrum on track gtexTissueExonMedianHeartLeftVentricl parent gtexExon shortLabel heartLeftVentricl longLabel Exon Expression in Heart - Left Ventricle from GTEx RNA-seq of 95 samples subGroups tissue=heartLeftVentricl color 139,26,168 spectrum on track gtexTissueExonMedianKidneyCortex parent gtexExon shortLabel kidneyCortex longLabel Exon Expression in Kidney - Cortex from GTEx RNA-seq of 8 samples subGroups tissue=kidneyCortex color 227,184,136 spectrum on track gtexTissueExonMedianLiver parent gtexExon shortLabel liver longLabel Exon Expression in Liver from GTEx RNA-seq of 34 samples subGroups tissue=liver color 227,184,136 spectrum on track gtexTissueExonMedianLung parent gtexExon shortLabel lung longLabel Exon Expression in Lung from GTEx RNA-seq of 133 samples subGroups tissue=lung color 167,243,12 spectrum on track gtexTissueExonMedianMinorSalivGland parent gtexExon shortLabel minorSalivGland longLabel Exon Expression in Minor Salivary Gland from GTEx RNA-seq of 5 samples subGroups tissue=minorSalivGland color 227,184,136 spectrum on track gtexTissueExonMedianMuscleSkeletal parent gtexExon shortLabel muscleSkeletal longLabel Exon Expression in Muscle - Skeletal from GTEx RNA-seq of 157 samples subGroups tissue=muscleSkeletal color 110,86,255 spectrum on track gtexTissueExonMedianNerveTibial parent gtexExon shortLabel nerveTibial longLabel Exon Expression in Nerve - Tibial from GTEx RNA-seq of 114 samples subGroups tissue=nerveTibial color 255,215,0 spectrum on track gtexTissueExonMedianOvary parent gtexExon shortLabel ovary longLabel Exon Expression in Ovary from GTEx RNA-seq of 35 samples subGroups tissue=ovary color 255,182,193 spectrum on track gtexTissueExonMedianPancreas parent gtexExon shortLabel pancreas longLabel Exon Expression in Pancreas from GTEx RNA-seq of 65 samples subGroups tissue=pancreas color 234,168,0 spectrum on track gtexTissueExonMedianPituitary parent gtexExon shortLabel pituitary longLabel Exon Expression in Pituitary from GTEx RNA-seq of 22 samples subGroups tissue=pituitary color 167,252,167 spectrum on track gtexTissueExonMedianProstate parent gtexExon shortLabel prostate longLabel Exon Expression in Prostate from GTEx RNA-seq of 42 samples subGroups tissue=prostate color 228,206,206 spectrum on track gtexTissueExonMedianSkinNotExposed parent gtexExon shortLabel skinNotExposed longLabel Exon Expression in Skin - Not Sun Exposed (Suprapubic) from GTEx RNA-seq of 41 samples subGroups tissue=skinNotExposed color 21,77,242 spectrum on track gtexTissueExonMedianSkinExposed parent gtexExon shortLabel skinExposed longLabel Exon Expression in Skin - Sun Exposed (Lower leg) from GTEx RNA-seq of 126 samples subGroups tissue=skinExposed color 30,144,255 spectrum on track gtexTissueExonMedianSmallIntestine parent gtexExon shortLabel smallIntestine longLabel Exon Expression in Small Intestine - Terminal Ileum from GTEx RNA-seq of 17 samples subGroups tissue=smallIntestine color 227,184,136 spectrum on track gtexTissueExonMedianSpleen parent gtexExon shortLabel spleen longLabel Exon Expression in Spleen from GTEx RNA-seq of 34 samples subGroups tissue=spleen color 227,184,136 spectrum on track gtexTissueExonMedianStomach parent gtexExon shortLabel stomach longLabel Exon Expression in Stomach from GTEx RNA-seq of 81 samples subGroups tissue=stomach color 255,211,155 spectrum on track gtexTissueExonMedianTestis parent gtexExon shortLabel testis longLabel Exon Expression in Testis from GTEx RNA-seq of 60 samples subGroups tissue=testis color 193,139,139 spectrum on track gtexTissueExonMedianThyroid parent gtexExon shortLabel thyroid longLabel Exon Expression in Thyroid from GTEx RNA-seq of 120 samples subGroups tissue=thyroid color 0,139,69 spectrum on track gtexTissueExonMedianUterus parent gtexExon shortLabel uterus longLabel Exon Expression in Uterus from GTEx RNA-seq of 36 samples subGroups tissue=uterus color 247,205,200 spectrum on track gtexTissueExonMedianVagina parent gtexExon shortLabel vagina longLabel Exon Expression in Vagina from GTEx RNA-seq of 34 samples subGroups tissue=vagina color 247,205,200 spectrum on track gtexTissueExonMedianWholeBlood parent gtexExon shortLabel wholeBlood longLabel Exon Expression in Whole Blood from GTEx RNA-seq of 191 samples subGroups tissue=wholeBlood color 255,0,255 spectrum on