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 G6PD
Basic gene info.Gene symbolG6PD
Gene nameglucose-6-phosphate dehydrogenase
SynonymsG6PD1
CytomapUCSC genome browser: Xq28
Genomic locationchrX :153759605-153775787
Type of geneprotein-coding
RefGenesNM_000402.4,
NM_001042351.2,
Ensembl idENSG00000269087
Descriptionglucose-6-phosphate 1-dehydrogenase
Modification date20141222
dbXrefs MIM : 305900
HGNC : HGNC
Ensembl : ENSG00000160211
HPRD : 02377
Vega : OTTHUMG00000024237
ProteinUniProt: P11413
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_G6PD
BioGPS: 2539
Gene Expression Atlas: ENSG00000269087
The Human Protein Atlas: ENSG00000269087
PathwayNCI Pathway Interaction Database: G6PD
KEGG: G6PD
REACTOME: G6PD
ConsensusPathDB
Pathway Commons: G6PD
MetabolismMetaCyc: G6PD
HUMANCyc: G6PD
RegulationEnsembl's Regulation: ENSG00000269087
miRBase: chrX :153,759,605-153,775,787
TargetScan: NM_000402
cisRED: ENSG00000269087
ContextiHOP: G6PD
cancer metabolism search in PubMed: G6PD
UCL Cancer Institute: G6PD
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of G6PD in cancer cell metabolism1. Martin-Bernabe A, Cortes R, Lehmann SG, Seve M, Cascante M, et al. (2014) Quantitative proteomic approach to understand metabolic adaptation in non-small cell lung cancer. J Proteome Res 13: 4695-4704. doi: 10.1021/pr500327v. go to article
2. D'Alessandro A, Amelio I, Berkers CR, Antonov A, Vousden KH, et al. (2014) Metabolic effect of TAp63alpha: enhanced glycolysis and pentose phosphate pathway, resulting in increased antioxidant defense. Oncotarget 5: 7722-7733. pmid: 4202156. go to article
3. Cai T, Kuang Y, Zhang C, Zhang Z, Chen L, et al. (2015) Glucose-6-phosphate dehydrogenase and NADPH oxidase 4 control STAT3 activity in melanoma cells through a pathway involving reactive oxygen species, c-SRC and SHP2. Am J Cancer Res 5: 1610-1620. pmid: 4497430. go to article
4. Coda DM, Lingua MF, Morena D, Foglizzo V, Bersani F, et al. (2015) SMYD1 and G6PD modulation are critical events for miR-206-mediated differentiation of rhabdomyosarcoma. Cell Cycle 14: 1389-1402. doi: 10.1080/15384101.2015.1005993. go to article
5. Aird KM, Worth AJ, Snyder NW, Lee JV, Sivanand S, et al. (2015) ATM couples replication stress and metabolic reprogramming during cellular senescence. Cell Rep 11: 893-901. doi: 10.1016/j.celrep.2015.04.014. pmid: 4431925. go to article

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Phenotypic Information for G6PD(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: G6PD
Familial Cancer Database: G6PD
* 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
KEGG_GLUTATHIONE_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 300908; phenotype.
305900; gene.
Orphanet 362; Glucose-6-phosphate-dehydrogenase deficiency.
DiseaseKEGG Disease: G6PD
MedGen: G6PD (Human Medical Genetics with Condition)
ClinVar: G6PD
PhenotypeMGI: G6PD (International Mouse Phenotyping Consortium)
PhenomicDB: G6PD

Mutations for G6PD
* 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 G6PD related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ352059G6PD168X153760922153761445G6PD64426X153761161153762335
CA419747ANAPC51810512121746160121746247G6PD105789X153760136153761273
M12996G6PD11671X153759627153763408PRKCA16642439176480606664806841
BE816962G6PD8152X153761181153761325G6PD145294X153761805153762319
BM688674G6PD1972X153759606153759659G6PD64236X153759955153760127

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=45)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr23:153761236-153761236p.D324D3
chr23:153760654-153760654p.Y437Y2
chr23:153760228-153760228p.P512H2
chr23:153760229-153760229p.P512S2
chr23:153762623-153762623p.R192C2
chr23:153760891-153760891p.R393L2
chr23:153762329-153762329p.A231T1
chr23:153761187-153761187p.V341I1
chr23:153763395-153763395p.C158F1
chr23:153761844-153761844p.V271M1

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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
# sample 11131 2 2  214  5218
# mutation 11121 2 2  215  52110
nonsynonymous SNV 1 121 1 2  215  41 7
synonymous SNV  1   1         1113
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
chrX:153762623p.R222C,G6PD2
chrX:153760228p.R423H,G6PD2
chrX:153760229p.P542H,G6PD2
chrX:153760891p.P542T,G6PD2
chrX:153760436p.Q225H,G6PD1
chrX:153764232p.R39Q,G6PD1
chrX:153761844p.R423R,G6PD1
chrX:153762658p.S38C,G6PD1
chrX:153760655p.S210F,G6PD1
chrX:153774257p.Q413H,G6PD1

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 G6PD 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 G6PD

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.
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check002.gifProtein Expression Plot (RPPA)
*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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

ACADL,AIFM1,AKR1C2,ALOX15B,DBI,ETFA,G6PD,
GGCT,GGT1,ISX,KPNA7,ME1,MPHOSPH6,MVK,
NSDHL,OXER1,PGD,POR,RLN3,SLED1,SPINK8
AACS,ABCC2,ADAM2,ALOX15B,DHRS2,FADS2,FDFT1,
FIBCD1,G6PD,GGT1,GGTLC2,HIST1H3D,HPGD,MVD,
MVK,NUDT8,PNLIPRP3,SERHL2,SERHL,SLC15A1,TARP

AIFM1,APEX2,ATP6AP1,BCAP31,CXorf40A,CXorf40B,EMD,
G6PD,GLA,IDH3G,IKBKG,IRAK1,KIF4A,LAS1L,
MTMR1,NSDHL,PRPS1,SLC10A3,SUV39H1,TMEM164,UBL4A
AP3D1,CARM1,CCNF,DPP9,FBXL19,G6PD,INCENP,
LIMK1,MAD1L1,MTA2,NACC1,RANGAP1,RPS6KA4,SART1,
SEC24C,TAPBP,TBC1D10B,TMEM104,TMEM214,TRIM56,VCP
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 G6PD
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P11413; -.
ChemistryChEMBL CHEMBL5347; -.
Organism-specific databasesPharmGKB PA28469; -.
Organism-specific databasesCTD 2539; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01582glucose-6-phosphate dehydrogenaseapprovedSulfamethazine
DB00608glucose-6-phosphate dehydrogenaseapprovedChloroquine
DB00250glucose-6-phosphate dehydrogenaseapproved; investigationalDapsone
DB01033glucose-6-phosphate dehydrogenaseapprovedMercaptopurine
DB00563glucose-6-phosphate dehydrogenaseapprovedMethotrexate
DB00783glucose-6-phosphate dehydrogenaseapproved; investigationalEstradiol
DB00675glucose-6-phosphate dehydrogenaseapprovedTamoxifen
DB01087glucose-6-phosphate dehydrogenaseapprovedPrimaquine


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Cross referenced IDs for G6PD
* 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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