Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 MVK
Basic gene info.Gene symbolMVK
Gene namemevalonate kinase
SynonymsLRBP|MK|MVLK|POROK3
CytomapUCSC genome browser: 12q24
Genomic locationchr12 :110011499-110035071
Type of geneprotein-coding
RefGenesNM_000431.3,
NM_001114185.2,NM_001301182.1,
Ensembl idENSG00000110921
DescriptionLH receptor mRNA-binding proteinmevalonate kinase 1
Modification date20141207
dbXrefs MIM : 251170
HGNC : HGNC
Ensembl : ENSG00000110921
HPRD : 02015
Vega : OTTHUMG00000169256
ProteinUniProt: Q03426
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MVK
BioGPS: 4598
Gene Expression Atlas: ENSG00000110921
The Human Protein Atlas: ENSG00000110921
PathwayNCI Pathway Interaction Database: MVK
KEGG: MVK
REACTOME: MVK
ConsensusPathDB
Pathway Commons: MVK
MetabolismMetaCyc: MVK
HUMANCyc: MVK
RegulationEnsembl's Regulation: ENSG00000110921
miRBase: chr12 :110,011,499-110,035,071
TargetScan: NM_000431
cisRED: ENSG00000110921
ContextiHOP: MVK
cancer metabolism search in PubMed: MVK
UCL Cancer Institute: MVK
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for MVK(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MVK
Familial Cancer Database: MVK
* 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_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 251170; gene.
260920; phenotype.
610377; phenotype.
Orphanet 29; Mevalonic aciduria.
343; Hyperimmunoglobulinemia D with periodic fever.
79152; Disseminated superficial actinic porokeratosis.
DiseaseKEGG Disease: MVK
MedGen: MVK (Human Medical Genetics with Condition)
ClinVar: MVK
PhenotypeMGI: MVK (International Mouse Phenotyping Consortium)
PhenomicDB: MVK

Mutations for MVK
* 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 MVK related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG698692TP6314313189597750189598181MVK42673612110034441110034754

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
There's no copy number variation information in COSMIC data for this gene.

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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=23)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=12)
Stat. for Insertions
(# total SNVs=0)
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
chr12:110019240-110019240p.A141fs*1811
chr12:110029077-110029077p.S267*2
chr12:110019222-110019222p.V132I2
chr12:110013947-110013947p.L75V2
chr12:110019277-110019277p.S150L2
chr12:110012694-110012694p.V23I2
chr12:110019327-110019328p.P167L1
chr12:110013833-110013833p.T37A1
chr12:110029057-110029057p.I260I1
chr12:110034308-110034308p.G373S1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  61      212  35 4
# mutation1  61      212  35 5
nonsynonymous SNV   41      2 1  35 2
synonymous SNV1  2        11     3
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
chr12:110019277p.S150L,MVK2
chr12:110019245p.V49V,MVK1
chr12:110032977p.I260I,MVK1
chr12:110013833p.N55T,MVK1
chr12:110034265p.G309G,MVK1
chr12:110013871p.P98L,MVK1
chr12:110019347p.R325H,MVK1
chr12:110013888p.D99N,MVK1
chr12:110023885p.G336S,MVK1
chr12:110017673p.A102D,MVK1

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 MVK 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 MVK

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

ACAA1,ALDH4A1,ALOX15B,ARRDC1,ERP29,GGT1,GGT3P,
GGTLC1,GUCY2D,HAAO,MMAB,MVK,NSDHL,OXER1,
PSMD9,SLC25A1,SLC26A6,SPINK8,TMEM150A,UGT2B28,UQCRC1
ADAM2,AFMID,AKR1A1,ALOX15B,DHCR7,DHRS2,EBP,
FDPS,G6PD,GGT1,GGTLC2,GUSB,HAAO,HIST1H3D,
HRASLS2,MVD,MVK,SERHL2,SERHL,SPINK8,SRD5A1

AACS,ACAT2,ALDH2,DHCR24,DHCR7,EBP,FDPS,
HMGCR,IDH1,LSS,MMAB,MVD,MVK,PLA2G3,
PRR13,SCARB1,SLC25A1,SLC25A3,TSFM,TUBA1C,WIBG
C14orf1,C6orf223,CYP51A1,DHCR7,FDFT1,FDPS,HMGCS1,
IDI1,INSIG1,LIPG,MVD,MVK,NSDHL,PCSK9,
PLA2G3,RDH11,MSMO1,SC5D,SQLE,STARD4,TEAD4
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 MVK
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryGuidetoPHARMACOLOGY 640; -.
Organism-specific databasesPharmGKB PA31331; -.
Organism-specific databasesCTD 4598; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB04695mevalonate kinaseexperimentalFARNESYL THIOPYROPHOSPHATE


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Cross referenced IDs for MVK
* 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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