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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 VRK1
check button Gene summary
Basic gene informationGene symbolVRK1
Gene namevaccinia related kinase 1
SynonymsPCH1|PCH1A
CytomapUCSC genome browser: 14q32
Type of geneprotein-coding
RefGenesNM_003384.2,
Descriptionserine/threonine-protein kinase VRK1vaccinia virus B1R-related kinase 1vaccinia-related kinase 1
Modification date20141207
dbXrefs MIM : 602168
HGNC : HGNC
Ensembl : ENSG00000100749
HPRD : 03701
Vega : OTTHUMG00000171459
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_VRK1
BioGPS: 7443
PathwayNCI Pathway Interaction Database: VRK1
KEGG: VRK1
REACTOME: VRK1
Pathway Commons: VRK1
ContextiHOP: VRK1
ligand binding site mutation search in PubMed: VRK1
UCL Cancer Institute: VRK1
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)BladderBone marrowTestis
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)BLCALAMLTGCT
Reference showing the relevant tissue of VRK1
Description by TissGene annotationsCancer gene
TissgsLTS
* 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
GO:0006468protein phosphorylation22194607
GO:0043987histone H3-S10 phosphorylation22194607
GO:0046777protein autophosphorylation21543316
GO:0072355histone H3-T3 phosphorylation22194607
GO:0090166Golgi disassembly19103756
GO:0006468protein phosphorylation22194607
GO:0043987histone H3-S10 phosphorylation22194607
GO:0046777protein autophosphorylation21543316
GO:0072355histone H3-T3 phosphorylation22194607
GO:0090166Golgi disassembly19103756


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TissGeneExp for VRK1

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
LUSC1.8493114140.4686741591.3806372557.27E-197.37E-18


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TissGene-miRNA for VRK1

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 VRK1
TissGeneSNV for VRK1

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.R219IUCEC2
p.K356EUCEC1
p.D273YESCA1
p.K359NLGG1
p.M303TSTAD1
p.R358XKIRC1
p.L195MKIRP1
p.L183FCESC1
p.E361*UCEC1
p.D231NLUAD1
p.E94KCESC1
p.K356NUCEC1
p.R203QUCEC1
p.K35NUCEC1
p.G176RMESO1
p.R203WSTAD1
p.G223DUCEC1
p.D120NBLCA1
p.E381KBLCA1
p.K269RUCEC1
p.V236LLUAD1
p.Q88LLUSC1
p.T102ISKCM1
p.R387CREAD1
p.R151WSKCM1
p.R133HUCEC1
p.R203WHNSC1
p.A20SBLCA1
p.K211QCOAD1
p.R160IREAD1
p.Y198CLGG1
p.C205YUCEC1
p.W99LLUAD1
p.E313KLGG1
p.G208VLUAD1
p.A9TBRCA1
p.I141MPAAD1
p.G123RSKCM1
p.R103CSARC1
p.G327*UCEC1


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TissGeneCNV for VRK1

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 VRK1

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
Chimerdb3.0ChiTaRsNAAA077909VRK1-ALOX5APchr14:97329031chr13:31318411
TCGAfusionPortalPRADAHNSCTCGA-HD-7753-01AVRK1-SAMD4AOut-of-frameChr14:97327072Chr14:55168780
TCGAfusionPortalPRADALUSCTCGA-34-5236-01AZFHX4-VRK1NAChr8:77620283Chr14:97397668


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TissGeneNet for VRK1

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)
VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (tumor)VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (normal)
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COAD (tumor)COAD (normal)
VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (tumor)VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (normal)
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HNSC (tumor)HNSC (normal)
VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (tumor)VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (normal)
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KICH (tumor)KICH (normal)
VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (tumor)VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (normal)
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KIRC (tumor)KIRC (normal)
VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (tumor)VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (normal)
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KIRP (tumor)KIRP (normal)
VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (tumor)VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (normal)
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LIHC (tumor)LIHC (normal)
VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (tumor)VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (normal)
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LUAD (tumor)LUAD (normal)
VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (tumor)VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (normal)
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LUSC (tumor)LUSC (normal)
VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (tumor)VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (normal)
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PRAD (tumor)PRAD (normal)
VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (tumor)VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (normal)
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STAD (tumor)STAD (normal)
VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (tumor)VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (normal)
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THCA (tumor)THCA (normal)
VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (tumor)VRK1, TP53, RCC1, COIL, JUN, SIRT3, RAN, ATF2, GOLGB1, HIST2H2BE, PLK3, TFAP4, VRK3 (normal)
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TissGeneProg for VRK1

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 VRK1
TissGeneDrug for VRK1

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 VRK1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0266468Congenital pontocerebellar hypoplasia5BeFree
umls:C1261175Pontoneocerebellar hypoplasia5BeFree
umls:C0026847Spinal Muscular Atrophy2BeFree
umls:C1843504Pontocerebellar Hypoplasia Type 12BeFree,CLINVAR,CTD_human,ORPHANET
umls:C0001418Adenocarcinoma1BeFree
umls:C0006142Malignant neoplasm of breast1BeFree
umls:C0007137Squamous cell carcinoma1BeFree
umls:C0019196Hepatitis C1LHGDN
umls:C0019348Herpes Simplex Infections1BeFree
umls:C0021390Inflammatory Bowel Diseases1GAD
umls:C0024121Lung Neoplasms1BeFree
umls:C0035335Retinoblastoma1BeFree
umls:C0266470Cerebellar Hypoplasia1BeFree
umls:C0596263Carcinogenesis1BeFree
umls:C0678222Breast Carcinoma1BeFree
umls:C0684249Carcinoma of lung1BeFree
umls:C3714756Intellectual Disability1CTD_human