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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 VTCN1
check button Gene summary
Basic gene informationGene symbolVTCN1
Gene nameV-set domain containing T cell activation inhibitor 1
SynonymsB7-H4|B7H4|B7S1|B7X|B7h.5|PRO1291|VCTN1
CytomapUCSC genome browser: 1p13.1
Type of geneprotein-coding
RefGenesNM_001253849.1,
NM_001253850.1,NM_024626.3,NR_045603.1,NR_045604.1,
DescriptionB7 family member, H4B7 homolog 4B7 superfamily member 1T cell costimulatory molecule B7xT-cell costimulatory molecule B7xV-set domain-containing T-cell activation inhibitor 1immune costimulatory protein B7-H4
Modification date20141207
dbXrefs MIM : 608162
HGNC : HGNC
Ensembl : ENSG00000134258
HPRD : 06429
Vega : OTTHUMG00000012118
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_VTCN1
BioGPS: 79679
PathwayNCI Pathway Interaction Database: VTCN1
KEGG: VTCN1
REACTOME: VTCN1
Pathway Commons: VTCN1
ContextiHOP: VTCN1
ligand binding site mutation search in PubMed: VTCN1
UCL Cancer Institute: VTCN1
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)BreastOvary
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)BRCAOV
Reference showing the relevant tissue of VTCN1
Description by TissGene annotationsCancer gene
Have significant anti-correlated miRNA
Fused withOncogene
* 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 VTCN1

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
THCA-0.047388927-3.5135092663.4661203391.21E-107.93E-10
LUSC2.501846998-0.6774824133.1793294122.38E-087.18E-08
PRAD0.5335099322.538742624-2.0052326926.60E-074.88E-06
KICH-2.0449964534.752007547-6.7970044.79E-192.71E-17
LIHC-1.6140344531.485191547-3.0992262.54E-082.02E-07
KIRC-1.3726971195.061415381-6.43411253.57E-411.57E-39
KIRP2.4727851725.007419547-2.5346343751.72E-071.01E-06
COAD-3.22910353-4.3015189141.0724153850.001410.003920444
LUAD1.216779892-0.5952580391.8120379315.17E-050.000135947


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TissGene-miRNA for VTCN1

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
ACChsa-miR-382-3pMIMAT00226970.0054-0.3278
ACChsa-miR-382-3pMIMAT00226970.0054-0.3278


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TissGeneMut for VTCN1
TissGeneSNV for VTCN1

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.F266LLIHC1
p.T38SHNSC1
p.S256LSKCM1
p.R116WGBM1
p.S65CBLCA1
p.E92QBLCA1
p.F96LREAD1
p.R100GBLCA1
p.R116QESCA1
p.E85KSKCM1
p.T41AKIRP1
p.R100QSTAD1
p.V120MLUAD1
p.L115SLGG1
p.P175SSKCM1
p.S269IGBM1
p.D230NSKCM1
p.L25FSKCM1
p.S3FSKCM1
p.N220SSKCM1
p.D135NSKCM1
p.E82ACOAD1
p.S148LCOAD1
p.S192LLUAD1
p.F191LPAAD1
p.R172*PRAD1
p.S135CHNSC1
p.E59KSKCM1
p.R248QSARC1
p.D189NCESC1
p.G148ESKCM1


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TissGeneCNV for VTCN1

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 VTCN1

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-E9-A244-01AVTCN1-NUP88Out-of-Framechr1:117695712chr17:5292280
Chimerdb3.0TopHat-FusionBRCATCGA-E9-A244-01AVTCN1-NUP88Out-of-Framechr1:117695712chr17:5292279
TCGAfusionPortalPRADABRCATCGA-E9-A244-01AVTCN1-NUP88Out-of-frameChr1:117695713Chr17:5292280
TCGAfusionPortalPRADAOVTCGA-29-1785-01AVTCN1-PTGFRNOut-of-frameChr1:117753446Chr1:117484337


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TissGeneNet for VTCN1

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)
VTCN1, BTLA (tumor)VTCN1, BTLA (normal)
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COAD (tumor)COAD (normal)
VTCN1, BTLA (tumor)VTCN1, BTLA (normal)
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HNSC (tumor)HNSC (normal)
VTCN1, BTLA (tumor)VTCN1, BTLA (normal)
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KICH (tumor)KICH (normal)
VTCN1, BTLA (tumor)VTCN1, BTLA (normal)
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KIRC (tumor)KIRC (normal)
VTCN1, BTLA (tumor)VTCN1, BTLA (normal)
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KIRP (tumor)KIRP (normal)
VTCN1, BTLA (tumor)VTCN1, BTLA (normal)
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LIHC (tumor)LIHC (normal)
VTCN1, BTLA (tumor)VTCN1, BTLA (normal)
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LUAD (tumor)LUAD (normal)
VTCN1, BTLA (tumor)VTCN1, BTLA (normal)
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LUSC (tumor)LUSC (normal)
VTCN1, BTLA (tumor)VTCN1, BTLA (normal)
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PRAD (tumor)PRAD (normal)
VTCN1, BTLA (tumor)VTCN1, BTLA (normal)
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STAD (tumor)STAD (normal)
VTCN1, BTLA (tumor)VTCN1, BTLA (normal)
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THCA (tumor)THCA (normal)
VTCN1, BTLA (tumor)VTCN1, BTLA (normal)
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TissGeneProg for VTCN1

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 VTCN1
TissGeneDrug for VTCN1

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status


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TissGeneDisease for VTCN1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0006142Malignant neoplasm of breast7BeFree,GAD
umls:C0178874Tumor Progression7BeFree
umls:C0678222Breast Carcinoma7BeFree
umls:C0024623Malignant neoplasm of stomach4BeFree
umls:C0029925Ovarian Carcinoma4BeFree
umls:C1140680Malignant neoplasm of ovary4BeFree
umls:C1519680Tumor Immunity4BeFree
umls:C0007134Renal Cell Carcinoma3BeFree,LHGDN
umls:C0235974Pancreatic carcinoma3BeFree
umls:C0346647Malignant neoplasm of pancreas3BeFree
umls:C0699791Stomach Carcinoma3BeFree
umls:C0003873Rheumatoid Arthritis2BeFree
umls:C0011847Diabetes2BeFree
umls:C0011849Diabetes Mellitus2BeFree
umls:C0027627Neoplasm Metastasis2BeFree
umls:C0596263Carcinogenesis2BeFree
umls:C0919267ovarian neoplasm2LHGDN
umls:C3495559Juvenile arthritis2BeFree,GAD
umls:C3714757Juvenile rheumatoid arthritis2BeFree
umls:C0001418Adenocarcinoma1BeFree
umls:C0003864Arthritis1GWASCAT
umls:C0004364Autoimmune Diseases1BeFree
umls:C0007847Malignant tumor of cervix1BeFree
umls:C0009402Colorectal Carcinoma1BeFree
umls:C0011854Diabetes Mellitus, Insulin-Dependent1BeFree
umls:C0014859Esophageal Neoplasms1BeFree
umls:C0017661IGA Glomerulonephritis1BeFree
umls:C0019159Hepatitis A1BeFree
umls:C0022658Kidney Diseases1BeFree
umls:C0024143Lupus Nephritis1BeFree
umls:C0025202melanoma1BeFree
umls:C0026764Multiple Myeloma1BeFree
umls:C0027697Nephritis1BeFree
umls:C0029463Osteosarcoma1BeFree
umls:C0085110Severe Combined Immunodeficiency1BeFree
umls:C0086445Idiopathic Membranous Glomerulonephritis1BeFree
umls:C0152018Esophageal carcinoma1BeFree
umls:C0206692Carcinoma, Lobular1BeFree
umls:C0242379Malignant neoplasm of lung1BeFree
umls:C0302592Cervix carcinoma1BeFree
umls:C0546837Malignant neoplasm of esophagus1BeFree
umls:C0585442Osteosarcoma of bone1BeFree
umls:C0677886Epithelial ovarian cancer1BeFree
umls:C0684249Carcinoma of lung1BeFree
umls:C0686619Secondary malignant neoplasm of lymph node1BeFree
umls:C0887833Carcinoma, Pancreatic Ductal1LHGDN
umls:C1176475Ductal Carcinoma1BeFree
umls:C1271104Blood pressure finding1GAD
umls:C1272641Systemic arterial pressure1GAD
umls:C1335302Pancreatic Ductal Adenocarcinoma1BeFree
umls:C1336076Sporadic Breast Carcinoma1BeFree
umls:C1512981Mammary Tumorigenesis1BeFree
umls:C1527249Colorectal Cancer1BeFree
umls:C3549742Breast cancer, lobular1BeFree