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| TissGeneSummary for VRK1 |
 Gene summary |
| Basic gene information | Gene symbol | VRK1 |
| Gene name | vaccinia related kinase 1 | |
| Synonyms | PCH1|PCH1A | |
| Cytomap | UCSC genome browser: 14q32 | |
| Type of gene | protein-coding | |
| RefGenes | NM_003384.2, | |
| Description | serine/threonine-protein kinase VRK1vaccinia virus B1R-related kinase 1vaccinia-related kinase 1 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 602168 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000100749 | ||
| HPRD : 03701 | ||
| Vega : OTTHUMG00000171459 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_VRK1 | |
| BioGPS: 7443 | ||
| Pathway | NCI Pathway Interaction Database: VRK1 | |
| KEGG: VRK1 | ||
| REACTOME: VRK1 | ||
| Pathway Commons: VRK1 | ||
| Context | iHOP: VRK1 | |
| ligand binding site mutation search in PubMed: VRK1 | ||
| UCL Cancer Institute: VRK1 | ||
| Assigned class in TissGDB* | C | |
| Included tissue-specific gene expression resources | TiGER,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 annotations | Cancer 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. |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO term | PubMed ID | GO:0006468 | protein phosphorylation | 22194607 | GO:0043987 | histone H3-S10 phosphorylation | 22194607 | GO:0046777 | protein autophosphorylation | 21543316 | GO:0072355 | histone H3-T3 phosphorylation | 22194607 | GO:0090166 | Golgi disassembly | 19103756 | GO:0006468 | protein phosphorylation | 22194607 | GO:0043987 | histone H3-S10 phosphorylation | 22194607 | GO:0046777 | protein autophosphorylation | 21543316 | GO:0072355 | histone H3-T3 phosphorylation | 22194607 | GO:0090166 | Golgi disassembly | 19103756 |
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| TissGeneExp for VRK1 |
| 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) |
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| 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) |
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| 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. |
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| 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) |
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| - Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
| Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
| LUSC | 1.849311414 | 0.468674159 | 1.380637255 | 7.27E-19 | 7.37E-18 |
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| TissGene-miRNA for VRK1 |
| 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 type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
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| TissGeneMut for VRK1 |
| TissGeneSNV for VRK1 |
| 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. |
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| 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) |
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| - nsSNVs sorted by frequency. |
| AAchange | Cancer type | # samples |
| p.R219I | UCEC | 2 |
| p.K356E | UCEC | 1 |
| p.D273Y | ESCA | 1 |
| p.K359N | LGG | 1 |
| p.M303T | STAD | 1 |
| p.R358X | KIRC | 1 |
| p.L195M | KIRP | 1 |
| p.L183F | CESC | 1 |
| p.E361* | UCEC | 1 |
| p.D231N | LUAD | 1 |
| p.E94K | CESC | 1 |
| p.K356N | UCEC | 1 |
| p.R203Q | UCEC | 1 |
| p.K35N | UCEC | 1 |
| p.G176R | MESO | 1 |
| p.R203W | STAD | 1 |
| p.G223D | UCEC | 1 |
| p.D120N | BLCA | 1 |
| p.E381K | BLCA | 1 |
| p.K269R | UCEC | 1 |
| p.V236L | LUAD | 1 |
| p.Q88L | LUSC | 1 |
| p.T102I | SKCM | 1 |
| p.R387C | READ | 1 |
| p.R151W | SKCM | 1 |
| p.R133H | UCEC | 1 |
| p.R203W | HNSC | 1 |
| p.A20S | BLCA | 1 |
| p.K211Q | COAD | 1 |
| p.R160I | READ | 1 |
| p.Y198C | LGG | 1 |
| p.C205Y | UCEC | 1 |
| p.W99L | LUAD | 1 |
| p.E313K | LGG | 1 |
| p.G208V | LUAD | 1 |
| p.A9T | BRCA | 1 |
| p.I141M | PAAD | 1 |
| p.G123R | SKCM | 1 |
| p.R103C | SARC | 1 |
| p.G327* | UCEC | 1 |
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| TissGeneCNV for VRK1 |
| 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) |
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| TissGeneFusions for VRK1 |
| Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
| Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
| Chimerdb3.0 | ChiTaRs | NA | AA077909 | VRK1-ALOX5AP | chr14:97329031 | chr13:31318411 | |
| TCGAfusionPortal | PRADA | HNSC | TCGA-HD-7753-01A | VRK1-SAMD4A | Out-of-frame | Chr14:97327072 | Chr14:55168780 |
| TCGAfusionPortal | PRADA | LUSC | TCGA-34-5236-01A | ZFHX4-VRK1 | NA | Chr8:77620283 | Chr14:97397668 |
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| TissGeneNet for VRK1 |
| 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 |
| 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. |
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| 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. |
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| 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. |
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| 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. |
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| TissGeneClin for VRK1 |
| TissGeneDrug for VRK1 |
| Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
| DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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| TissGeneDisease for VRK1 |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0266468 | Congenital pontocerebellar hypoplasia | 5 | BeFree |
| umls:C1261175 | Pontoneocerebellar hypoplasia | 5 | BeFree |
| umls:C0026847 | Spinal Muscular Atrophy | 2 | BeFree |
| umls:C1843504 | Pontocerebellar Hypoplasia Type 1 | 2 | BeFree,CLINVAR,CTD_human,ORPHANET |
| umls:C0001418 | Adenocarcinoma | 1 | BeFree |
| umls:C0006142 | Malignant neoplasm of breast | 1 | BeFree |
| umls:C0007137 | Squamous cell carcinoma | 1 | BeFree |
| umls:C0019196 | Hepatitis C | 1 | LHGDN |
| umls:C0019348 | Herpes Simplex Infections | 1 | BeFree |
| umls:C0021390 | Inflammatory Bowel Diseases | 1 | GAD |
| umls:C0024121 | Lung Neoplasms | 1 | BeFree |
| umls:C0035335 | Retinoblastoma | 1 | BeFree |
| umls:C0266470 | Cerebellar Hypoplasia | 1 | BeFree |
| umls:C0596263 | Carcinogenesis | 1 | BeFree |
| umls:C0678222 | Breast Carcinoma | 1 | BeFree |
| umls:C0684249 | Carcinoma of lung | 1 | BeFree |
| umls:C3714756 | Intellectual Disability | 1 | CTD_human |
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