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 NQO1
Basic gene info.Gene symbolNQO1
Gene nameNAD(P)H dehydrogenase, quinone 1
SynonymsDHQU|DIA4|DTD|NMOR1|NMORI|QR1
CytomapUCSC genome browser: 16q22.1
Genomic locationchr16 :69743303-69760533
Type of geneprotein-coding
RefGenesNM_000903.2,
NM_001025433.1,NM_001025434.1,NM_001286137.1,
Ensembl idENSG00000181019
DescriptionDT-diaphoraseNAD(P)H dehydrogenase [quinone] 1NAD(P)H:Quinone acceptor oxidoreductase type 1NAD(P)H:menadione oxidoreductase 1NAD(P)H:quinone oxidoreductase 1NAD(P)H:quinone oxireductaseazoreductasediaphorase (NADH/NADPH) (cytochrome b-5 reductase)
Modification date20141222
dbXrefs MIM : 125860
HGNC : HGNC
Ensembl : ENSG00000181019
HPRD : 00518
Vega : OTTHUMG00000137575
ProteinUniProt: P15559
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NQO1
BioGPS: 1728
Gene Expression Atlas: ENSG00000181019
The Human Protein Atlas: ENSG00000181019
PathwayNCI Pathway Interaction Database: NQO1
KEGG: NQO1
REACTOME: NQO1
ConsensusPathDB
Pathway Commons: NQO1
MetabolismMetaCyc: NQO1
HUMANCyc: NQO1
RegulationEnsembl's Regulation: ENSG00000181019
miRBase: chr16 :69,743,303-69,760,533
TargetScan: NM_000903
cisRED: ENSG00000181019
ContextiHOP: NQO1
cancer metabolism search in PubMed: NQO1
UCL Cancer Institute: NQO1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for NQO1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NQO1
Familial Cancer Database: NQO1
* 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_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM 125860; gene.
Orphanet
DiseaseKEGG Disease: NQO1
MedGen: NQO1 (Human Medical Genetics with Condition)
ClinVar: NQO1
PhenotypeMGI: NQO1 (International Mouse Phenotyping Consortium)
PhenomicDB: NQO1

Mutations for NQO1
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasNQO1chr166974497469744994CHST3chr107375573573755755
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NQO1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA648735SNHG617586783470967834783NQO176546166974893469760463
BM755010NQO117136166976033669760461TTC3713648259481408294820550
CB159668NQO11121166974700169748955NQO1116565166974480569747000
BQ220009FAM155A8513613108363673108363730NQO1131866166974331669744046
BM983726NQO118191166974474969744922DYRK1A184279213888737938887473
DB537013NQO11297166974422169744518XRN12973313142053702142053736
BU189113NQO11493166974429969744378NQO190859166974355869744323

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=15)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
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
chr16:69752312-69752312p.M45L2
chr16:69745073-69745073p.R211C2
chr16:69745102-69745102p.R201Q2
chr16:69745145-69745145p.P187S2
chr16:69746953-69746953p.N166T1
chr16:69752310-69752310p.M45I1
chr16:69744882-69744882p.K274K1
chr16:69746966-69746966p.H162N1
chr16:69744887-69744887p.R273G1
chr16:69746978-69746978p.L158M1

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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
# sample 1 2       31   13 4
# mutation 1 2       51   13 6
nonsynonymous SNV 1 1       2    13 3
synonymous SNV   1       31      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
chr16:69746984p.K59K,NQO11
chr16:69744882p.K202K,NQO11
chr16:69746985p.L42L,NQO11
chr16:69744912p.I192M,NQO11
chr16:69748870p.A29T,NQO11
chr16:69744936p.V184V,NQO11
chr16:69748892p.K23N,NQO11
chr16:69744945p.G181G,NQO11
chr16:69752137p.W144L,NQO11
chr16:69745057p.R139C,NQO11

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 NQO1 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 NQO1

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

AP1G1,ATP6V0D1,C16orf70,CDH1,COG4,COG8,CTCF,
CYB5B,ESRP2,EXOSC6,FAM192A,G6PD,GOT2,HSBP1,
IST1,ME1,NQO1,ORMDL2,POLR2C,SQSTM1,UGT1A6
ABCC2,ADAM2,AWAT2,C6orf223,DHRS2,FAR2,G6PD,
HIST1H2BC,HPGD,HSD3B1,NQO1,PAPSS2,PNLIPRP3,SCP2,
SERHL2,SLC5A11,TARP,TMCC3,TMPRSS11F,TSKU,UGT2B28

AK1,ANXA4,ANXA9,TLDC2,CYSTM1,CLRN3,COPZ1,
HEBP2,MAPK3,METTL7B,MGST2,MGST3,NQO1,OSGIN1,
PNKD,SQSTM1,TM4SF5,TMCO1,EMC3,VDAC1,YIPF4
ABHD5,ASB11,CA2,CSN1S1,CSTB,CYP2B7P,MICU2,
ETNK1,GDPD3,IQCD,NQO1,OASL,SLC25A24,SLC25A33,
SLC4A9,SRI,TAT,TMEM56,TPMT,UBE2A,UGDH
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 NQO1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P15559; -.
ChemistryChEMBL CHEMBL3623; -.
Organism-specific databasesPharmGKB PA31744; -.
Organism-specific databasesCTD 1728; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00170NAD(P)H dehydrogenase, quinone 1approved; nutraceuticalMenadione
DB00266NAD(P)H dehydrogenase, quinone 1approvedDicumarol
DB01927NAD(P)H dehydrogenase, quinone 1experimentalDuroquinone
DB02395NAD(P)H dehydrogenase, quinone 1experimental3-Hydroxymethyl-5-Aziridinyl-1methyl-2-[1h-Indole-4,7-Dione]-Propanol
DB02400NAD(P)H dehydrogenase, quinone 1experimental5-Methoxy-1,2-Dimethyl-3-(4-Nitrophenoxymethyl)Indole-4,7-Dione
DB02633NAD(P)H dehydrogenase, quinone 1experimentalCibacron Blue
DB03147NAD(P)H dehydrogenase, quinone 1experimentalFlavin-Adenine Dinucleotide
DB03626NAD(P)H dehydrogenase, quinone 1experimental5-Methoxy-1,2-Dimethyl-3-(Phenoxymethyl)Indole-4,7-Dione
DB04090NAD(P)H dehydrogenase, quinone 1experimental2,5-Diaziridin-1-Yl-3-(Hydroxymethyl)-6-Methylcyclohexa-2,5-Diene-1,4-Dione
DB04392NAD(P)H dehydrogenase, quinone 1experimentalBishydroxy[2h-1-Benzopyran-2-One,1,2-Benzopyrone]
DB07385NAD(P)H dehydrogenase, quinone 1experimental3-(HYDROXYMETHYL)-1-METHYL-5-(2-METHYLAZIRIDIN-1-YL)-2-PHENYL-1H-INDOLE-4,7-DIONE
DB00818NAD(P)H dehydrogenase, quinone 1approved; investigationalPropofol
DB00997NAD(P)H dehydrogenase, quinone 1approved; investigationalDoxorubicin
DB00515NAD(P)H dehydrogenase, quinone 1approvedCisplatin
DB00305NAD(P)H dehydrogenase, quinone 1approvedMitomycin
DB00773NAD(P)H dehydrogenase, quinone 1approvedEtoposide
DB00445NAD(P)H dehydrogenase, quinone 1approvedEpirubicin
DB03033NAD(P)H dehydrogenase, quinone 1experimental1-Methyloxy-4-Sulfone-Benzene
DB01022NAD(P)H dehydrogenase, quinone 1approvedPhytonadione


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Cross referenced IDs for NQO1
* 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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