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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for VKORC1 |
Basic gene info. | Gene symbol | VKORC1 |
Gene name | vitamin K epoxide reductase complex, subunit 1 | |
Synonyms | EDTP308|IMAGE3455200|MST134|MST576|VKCFD2|VKOR | |
Cytomap | UCSC genome browser: 16p11.2 | |
Genomic location | chr16 :31102174-31106276 | |
Type of gene | protein-coding | |
RefGenes | NM_024006.4, NM_206824.1, | |
Ensembl id | ENSG00000255439 | |
Description | phylloquinone epoxide reductasevitamin K dependent clotting factors deficiency 2vitamin K epoxide reductase complex subunit 1vitamin K1 2,3-epoxide reductase subunit 1vitamin K1 epoxide reductase (warfarin-sensitive) | |
Modification date | 20141207 | |
dbXrefs | MIM : 608547 | |
HGNC : HGNC | ||
Ensembl : ENSG00000167397 | ||
HPRD : 10540 | ||
Vega : OTTHUMG00000047408 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_VKORC1 | |
BioGPS: 79001 | ||
Gene Expression Atlas: ENSG00000255439 | ||
The Human Protein Atlas: ENSG00000255439 | ||
Pathway | NCI Pathway Interaction Database: VKORC1 | |
KEGG: VKORC1 | ||
REACTOME: VKORC1 | ||
ConsensusPathDB | ||
Pathway Commons: VKORC1 | ||
Metabolism | MetaCyc: VKORC1 | |
HUMANCyc: VKORC1 | ||
Regulation | Ensembl's Regulation: ENSG00000255439 | |
miRBase: chr16 :31,102,174-31,106,276 | ||
TargetScan: NM_024006 | ||
cisRED: ENSG00000255439 | ||
Context | iHOP: VKORC1 | |
cancer metabolism search in PubMed: VKORC1 | ||
UCL Cancer Institute: VKORC1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for VKORC1(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: VKORC1 |
Familial Cancer Database: VKORC1 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
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REACTOME_METABOLISM_OF_PROTEINS |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: VKORC1 |
MedGen: VKORC1 (Human Medical Genetics with Condition) | |
ClinVar: VKORC1 | |
Phenotype | MGI: VKORC1 (International Mouse Phenotyping Consortium) |
PhenomicDB: VKORC1 |
Mutations for VKORC1 |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows VKORC1 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 2 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 2 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
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Stat. for Non-Synonymous SNVs (# total SNVs=6) | (# total SNVs=4) |
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(# total SNVs=0) | (# total SNVs=0) |
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* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr16:31105994-31105994 | p.G19G | 2 |
chr16:31105909-31105909 | p.A48T | 1 |
chr16:31102480-31102480 | p.P156H | 1 |
chr16:31105925-31105925 | p.L42L | 1 |
chr16:31102501-31102501 | p.S149T | 1 |
chr16:31105974-31105974 | p.A26V | 1 |
chr16:31102541-31102541 | p.I136V | 1 |
chr16:31102602-31102602 | p.A115A | 1 |
chr16:31105997-31105997 | p.T18T | 1 |
chr16:31102655-31102655 | p.R98W | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 | 2 |   |   |   |   | 1 |   | 1 |   |   | 2 |   |   |   |   |   | 2 |   | 1 |
# mutation | 1 | 2 |   |   |   |   | 1 |   | 1 |   |   | 2 |   |   |   |   |   | 2 |   | 1 |
nonsynonymous SNV | 1 |   |   |   |   |   |   |   | 1 |   |   | 1 |   |   |   |   |   |   |   | 1 |
synonymous SNV |   | 2 |   |   |   |   | 1 |   |   |   |   | 1 |   |   |   |   |   | 2 |   |   |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr16:31102461 | p.R162R | 1 |
chr16:31102480 | p.P156H | 1 |
chr16:31102541 | p.I136V | 1 |
chr16:31104640 | p.L92L | 1 |
chr16:31104693 | p.I75L | 1 |
chr16:31104726 | p.G64W | 1 |
chr16:31104727 | p.F63F | 1 |
chr16:31105880 | p.S57S,VKORC1 | 1 |
chr16:31105904 | p.I49I,VKORC1 | 1 |
chr16:31105925 | p.L42L,VKORC1 | 1 |
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* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
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cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for VKORC1 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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AP2S1,B4GALT7,BCL7C,TSR3,C1orf86,PRADC1,LAMTOR4, GUK1,HCFC1R1,JOSD2,MPG,MRPL28,MRPL53,NUDT1, RABAC1,SIVA1,SPNS1,TCEB2,VKORC1,ZNF668,ZNHIT1 | ATP6V1F,CAPNS1,CD63,CDIPT,CST3,EFEMP2,OST4, POLE4,PRKCDBP,RABAC1,RHOG,RNASEK,RNF181,S100A6, SERF2,SH3BGRL3,TAF10,TAX1BP3,TMSB10,TNFSF12,VKORC1 | ||||
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FAM212A,FAM229B,CERCAM,CHST14,CLEC11A,CMTM3,EFEMP2, EMP3,EVA1B,FAM195B,FAM89B,HCFC1R1,HOPX,IGFBP7, ILK,LGALS1,RAB34,SELM,TXNDC15,UBTD1,VKORC1 | ALDH1A1,AQP1,ATP5SL,CDR2L,CITED1,CYB5A,CYP2U1, DGCR6,KIFC3,LHPP,MAOB,PLA2G4C,PMP22,PRSS53, SFXN3,SH3GL1,SLC16A4,SLC2A12,TMEM25,TRIM32,VKORC1 |
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* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Pharmacological Information for VKORC1 |
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DB Category | DB Name | DB's ID and Url link |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00170 | vitamin K epoxide reductase complex, subunit 1 | approved; nutraceutical | Menadione | ![]() | ![]() |
DB00266 | vitamin K epoxide reductase complex, subunit 1 | approved | Dicumarol | ![]() | ![]() |
DB00498 | vitamin K epoxide reductase complex, subunit 1 | approved | Phenindione | ![]() | ![]() |
DB00682 | vitamin K epoxide reductase complex, subunit 1 | approved | Warfarin | ![]() | ![]() |
DB00946 | vitamin K epoxide reductase complex, subunit 1 | approved | Phenprocoumon | ![]() | ![]() |
DB01418 | vitamin K epoxide reductase complex, subunit 1 | approved | Acenocoumarol | ![]() | ![]() |
DB01118 | vitamin K epoxide reductase complex, subunit 1 | approved; investigational | Amiodarone | ![]() | ![]() |
DB00641 | vitamin K epoxide reductase complex, subunit 1 | approved | Simvastatin | ![]() | ![]() |
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Cross referenced IDs for VKORC1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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