Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for VKORC1
Basic gene info.Gene symbolVKORC1
Gene namevitamin K epoxide reductase complex, subunit 1
SynonymsEDTP308|IMAGE3455200|MST134|MST576|VKCFD2|VKOR
CytomapUCSC genome browser: 16p11.2
Genomic locationchr16 :31102174-31106276
Type of geneprotein-coding
RefGenesNM_024006.4,
NM_206824.1,
Ensembl idENSG00000255439
Descriptionphylloquinone 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 date20141207
dbXrefs MIM : 608547
HGNC : HGNC
Ensembl : ENSG00000167397
HPRD : 10540
Vega : OTTHUMG00000047408
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_VKORC1
BioGPS: 79001
Gene Expression Atlas: ENSG00000255439
The Human Protein Atlas: ENSG00000255439
PathwayNCI Pathway Interaction Database: VKORC1
KEGG: VKORC1
REACTOME: VKORC1
ConsensusPathDB
Pathway Commons: VKORC1
MetabolismMetaCyc: VKORC1
HUMANCyc: VKORC1
RegulationEnsembl's Regulation: ENSG00000255439
miRBase: chr16 :31,102,174-31,106,276
TargetScan: NM_024006
cisRED: ENSG00000255439
ContextiHOP: VKORC1
cancer metabolism search in PubMed: VKORC1
UCL Cancer Institute: VKORC1
Assigned class in ccmGDBC

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Phenotypic Information for VKORC1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: VKORC1
Familial Cancer Database: VKORC1
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: VKORC1
MedGen: VKORC1 (Human Medical Genetics with Condition)
ClinVar: VKORC1
PhenotypeMGI: 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows VKORC1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2                
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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=6)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* 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 positionMutation(aa)Unique sampleID count
chr16:31105994-31105994p.G19G2
chr16:31105909-31105909p.A48T1
chr16:31102480-31102480p.P156H1
chr16:31105925-31105925p.L42L1
chr16:31102501-31102501p.S149T1
chr16:31105974-31105974p.A26V1
chr16:31102541-31102541p.I136V1
chr16:31102602-31102602p.A115A1
chr16:31105997-31105997p.T18T1
chr16:31102655-31102655p.R98W1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12    1 1  2     2 1
# mutation12    1 1  2     2 1
nonsynonymous SNV1       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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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* 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 PositionMutation(aa)Unique sampleID count
chr16:31102461p.R162R1
chr16:31102480p.P156H1
chr16:31102541p.I136V1
chr16:31104640p.L92L1
chr16:31104693p.I75L1
chr16:31104726p.G64W1
chr16:31104727p.F63F1
chr16:31105880p.S57S,VKORC11
chr16:31105904p.I49I,VKORC11
chr16:31105925p.L42L,VKORC11

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for VKORC1 in TCGA
* 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.
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

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* 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

: Open all plots for all cancer types

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

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
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* 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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for VKORC1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00170vitamin K epoxide reductase complex, subunit 1approved; nutraceuticalMenadione
DB00266vitamin K epoxide reductase complex, subunit 1approvedDicumarol
DB00498vitamin K epoxide reductase complex, subunit 1approvedPhenindione
DB00682vitamin K epoxide reductase complex, subunit 1approvedWarfarin
DB00946vitamin K epoxide reductase complex, subunit 1approvedPhenprocoumon
DB01418vitamin K epoxide reductase complex, subunit 1approvedAcenocoumarol
DB01118vitamin K epoxide reductase complex, subunit 1approved; investigationalAmiodarone
DB00641vitamin K epoxide reductase complex, subunit 1approvedSimvastatin


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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

: Open all cross reference information



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