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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for PAH
check button Gene summary
Basic gene informationGene symbolPAH
Gene name
Synonyms
CytomapUCSC genome browser:
Type of gene
RefGenes
Description
Modification date
dbXrefs
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PAH
BioGPS: 101929036
PathwayNCI Pathway Interaction Database: PAH
KEGG: PAH
REACTOME: PAH
Pathway Commons: PAH
ContextiHOP: PAH
ligand binding site mutation search in PubMed: PAH
UCL Cancer Institute: PAH
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)KidneyLiver
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)KIRC,KIRP,KICHLIHC
Reference showing the relevant tissue of PAH
Description by TissGene annotationsCancer gene
Significant down-regulated DEG
TissgsKTS
CNV lost TissGeneKTS
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID


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TissGeneExp for PAH

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
LUAD-1.880464663-4.056600872.1761362071.76E-076.65E-07
LIHC8.9425371310.44170113-1.4991641.05E-054.41E-05
KIRP1.3246522556.61934288-5.2946906256.94E-073.64E-06
COAD-0.990397024-4.0760277933.0856307696.60E-063.14E-05
THCA-2.619962734-1.267423751-1.3525389835.65E-092.91E-08
KIRC1.6901352415.260379685-3.5702444448.23E-082.31E-07
KICH-0.154498874.91643313-5.0709324.83E-061.61E-05
LUSC-2.948829301-4.0030802821.054250980.0005850.001125038


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TissGene-miRNA for PAH

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for PAH
TissGeneSNV for PAH

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)

* Click on the image to enlarge it in a new window.
SNV lollipop
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.S303FSKCM3
p.P211SSKCM3
p.R111QBLCA2
p.E305KSKCM2
p.D415NSKCM2
p.V329LLUAD1
p.R111QSKCM1
p.Y216NBLCA1
p.R241CSTAD1
p.G257DLGG1
p.L213FLUAD1
p.E319XKIRC1
p.V190LCOAD1
p.R261*BLCA1
p.L365FSKCM1
p.R243*SKCM1
p.K215MCOAD1
p.I94TBLCA1
p.S196FSKCM1
p.R408WSKCM1
p.V45DKIRC1
p.R130KREAD1
p.A322TSARC1
p.F191CCESC1
p.A322VSTAD1
p.G442RREAD1
p.K274MGBM1
p.P69SBRCA1
p.E78DCOAD1
p.A104DDLBC1
p.G272RHNSC1
p.R53CPAAD1
p.G289RSKCM1
p.E286KSKCM1
p.K335EESCA1
p.K192NSTAD1
p.E221KSKCM1
p.D143YLUAD1
p.V412AKIRP1
p.F299YLUAD1
p.T193ILIHC1
p.L62RESCA1
p.T186PSTAD1
p.E182KREAD1
p.L444FSKCM1
p.P279LLUAD1
p.E422KSKCM1
p.P409HBRCA1
p.I125FKIRP1
p.G344SLUAD1
p.A373VESCA1
p.S295LESCA1
p.V153GHNSC1
p.E316KSKCM1
p.A447VHNSC1
p.R111QUCEC1
p.G10SCOAD1
p.S23ISTAD1
p.L385PLUSC1
p.R261QSKCM1
p.E214*BLCA1
p.E228KREAD1
p.E319*KIRC1
p.R297CUCEC1
p.R400TESCA1
p.D425NBLCA1
p.R243*OV1
p.T236SHNSC1
p.S16FLIHC1
p.S67CREAD1
p.V423ACOAD1
p.R408WPRAD1
p.C445FREAD1
p.H290YHNSC1
p.M180LBLCA1
p.F80ISKCM1
p.R71HBLCA1
p.S40LBLCA1
p.F210YKIRP1
p.A395SLUSC1
p.E280KGBM1
p.L136ICOAD1
p.E368KSARC1
p.D151YCOAD1
p.R270THNSC1
p.P9QSKCM1
p.G247SLUSC1
p.K398NSKCM1
p.E381KSKCM1


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TissGeneCNV for PAH

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for PAH

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0FusionScanBRCATCGA-BH-A0B7-01AEEA1-PAHIn-Framechr12:93258635chr12:103249110
TCGAfusionPortalPRADABRCATCGA-BH-A0B7-01AEEA1-PAHIn-frameChr12:93258636Chr12:103249110
TCGAfusionPortalPRADABRCATCGA-OL-A66I-01APAH-NINJ2In-frameChr12:103306569Chr12:675344
TCGAfusionPortalPRADAPRADTCGA-XQ-A8TA-01AANAPC7-PAHOut-of-frameChr12:110841332Chr12:103271328


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TissGeneNet for PAH

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)
BRCA (tumor)BRCA (normal)
PAH, PCBD1, RPS24, QDPR (tumor)PAH, PCBD1, RPS24, QDPR (normal)
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COAD (tumor)COAD (normal)
PAH, PCBD1, RPS24, QDPR (tumor)PAH, PCBD1, RPS24, QDPR (normal)
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HNSC (tumor)HNSC (normal)
PAH, PCBD1, RPS24, QDPR (tumor)PAH, PCBD1, RPS24, QDPR (normal)
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KICH (tumor)KICH (normal)
PAH, PCBD1, RPS24, QDPR (tumor)PAH, PCBD1, RPS24, QDPR (normal)
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KIRC (tumor)KIRC (normal)
PAH, PCBD1, RPS24, QDPR (tumor)PAH, PCBD1, RPS24, QDPR (normal)
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KIRP (tumor)KIRP (normal)
PAH, PCBD1, RPS24, QDPR (tumor)PAH, PCBD1, RPS24, QDPR (normal)
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LIHC (tumor)LIHC (normal)
PAH, PCBD1, RPS24, QDPR (tumor)PAH, PCBD1, RPS24, QDPR (normal)
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LUAD (tumor)LUAD (normal)
PAH, PCBD1, RPS24, QDPR (tumor)PAH, PCBD1, RPS24, QDPR (normal)
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LUSC (tumor)LUSC (normal)
PAH, PCBD1, RPS24, QDPR (tumor)PAH, PCBD1, RPS24, QDPR (normal)
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PRAD (tumor)PRAD (normal)
PAH, PCBD1, RPS24, QDPR (tumor)PAH, PCBD1, RPS24, QDPR (normal)
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STAD (tumor)STAD (normal)
PAH, PCBD1, RPS24, QDPR (tumor)PAH, PCBD1, RPS24, QDPR (normal)
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THCA (tumor)THCA (normal)
PAH, PCBD1, RPS24, QDPR (tumor)PAH, PCBD1, RPS24, QDPR (normal)
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TissGeneProg for PAH

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for PAH
TissGeneDrug for PAH

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status
DB00368NorepinephrineInhibitorSmall moleculeApproved
DB00360SapropterinCofactorSmall moleculeApproved|Investigational
DB06262DroxidopaInhibitorSmall moleculeApproved|Investigational
DB00120L-PhenylalanineSmall moleculeApproved|Nutraceutical
DB00668EpinephrineAntagonistSmall moleculeApproved|Vet_approved


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TissGeneDisease for PAH

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0031485Phenylketonurias269BeFree,CLINVAR,CTD_human,GAD,LHGDN
umls:C0751434Classical phenylketonuria255BeFree,GAD,MGD,ORPHANET,UNIPROT
umls:C0751435Hyperphenylalaninaemia104BeFree,CLINVAR,GAD
umls:C0025517Metabolic Diseases13BeFree
umls:C0085547Phenylketonuria, Maternal8BeFree,ORPHANET
umls:C0023903Liver neoplasms7BeFree
umls:C2239176Liver carcinoma7BeFree
umls:C0006142Malignant neoplasm of breast6BeFree
umls:C0036341Schizophrenia6BeFree,GAD
umls:C0152171Idiopathic pulmonary hypertension6BeFree
umls:C0242379Malignant neoplasm of lung6BeFree
umls:C0678222Breast Carcinoma6BeFree
umls:C0684249Carcinoma of lung6BeFree
umls:C0596263Carcinogenesis5BeFree
umls:C0025362Mental Retardation4BeFree
umls:C0025521Inborn Errors of Metabolism4BeFree
umls:C0036857Severe mental retardation (I.Q. 20-34)4BeFree
umls:C2973725Pulmonary arterial hypertension4BeFree
umls:C3714844Pulmonary Hypertension, Primary, 1, With Hereditary Hemorrhagic Telangiectasia4BeFree
umls:C0002514Amino Acid Metabolism, Inborn Errors3BeFree
umls:C0004352Autistic Disorder3BeFree,GAD
umls:C0015230Exanthema3BeFree
umls:C0268463Persistent hyperphenylalaninemia3BeFree
umls:C0848332Spots on skin3BeFree
umls:C0858970Carcinogenicity3BeFree
umls:C0004936Mental disorders2BeFree
umls:C0005684Malignant neoplasm of urinary bladder2BeFree
umls:C0011253Delusions2BeFree
umls:C0016952Galactosemias2BeFree,GAD
umls:C0018524Hallucinations2BeFree,GAD
umls:C0042900Vitiligo2BeFree
umls:C0231367Activity intolerance2BeFree
umls:C0279626Squamous cell carcinoma of esophagus2BeFree
umls:C0699885Carcinoma of bladder2BeFree
umls:C1847835VITILIGO-ASSOCIATED MULTIPLE AUTOIMMUNE DISEASE SUSCEPTIBILITY 1 (finding)2BeFree
umls:C3203102Idiopathic pulmonary arterial hypertension2BeFree
umls:C0004096Asthma1BeFree
umls:C0004134Ataxia1BeFree
umls:C0007102Malignant tumor of colon1BeFree
umls:C0007131Non-Small Cell Lung Carcinoma1BeFree
umls:C0010674Cystic Fibrosis1BeFree
umls:C0014859Esophageal Neoplasms1BeFree
umls:C0020459Hyperinsulinism1BeFree
umls:C0021051Immunologic Deficiency Syndromes1BeFree
umls:C0024408Machado-Joseph Disease1BeFree
umls:C0025322Premature Menopause1BeFree
umls:C0027498Nausea and vomiting1BeFree
umls:C0030587Paroxysmal atrial tachycardia1BeFree
umls:C0041341Tuberous Sclerosis1BeFree
umls:C0042373Vascular Diseases1BeFree
umls:C0152018Esophageal carcinoma1BeFree
umls:C0152021Congenital heart disease1BeFree
umls:C0152115Lingual-Facial-Buccal Dyskinesia1BeFree,GAD
umls:C0162429Malnutrition1BeFree
umls:C0162739HELLP Syndrome1BeFree
umls:C0235031Neurologic Symptoms1BeFree
umls:C0264408Childhood asthma1BeFree
umls:C0268151Classical galactosemia1BeFree
umls:C0339573Glaucoma, Primary Open Angle1BeFree
umls:C0376358Malignant neoplasm of prostate1GAD
umls:C0393610Dystonia, Diurnal1BeFree
umls:C0524620Metabolic Syndrome X1BeFree
umls:C0546837Malignant neoplasm of esophagus1BeFree
umls:C0686347Tardive Dyskinesia1BeFree,GAD
umls:C0699790Colon Carcinoma1BeFree
umls:C0747102Ovarian failure1BeFree
umls:C1851920Dopa-Responsive Dystonia1BeFree
umls:C3714756Intellectual Disability1BeFree
umls:C2678416Hyperphenylalaninemia, Non-Pku Mild0CLINVAR