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 GPX3
Basic gene info.Gene symbolGPX3
Gene nameglutathione peroxidase 3 (plasma)
SynonymsGPx-P|GSHPx-3|GSHPx-P
CytomapUCSC genome browser: 5q23
Genomic locationchr5 :150399998-150408554
Type of geneprotein-coding
RefGenesNM_002084.3,
Ensembl idENSG00000211445
DescriptionGPx-3extracellular glutathione peroxidaseglutathione peroxidase 3plasma glutathione peroxidase
Modification date20141222
dbXrefs MIM : 138321
HGNC : HGNC
Ensembl : ENSG00000211445
HPRD : 11750
Vega : OTTHUMG00000163693
ProteinUniProt: P22352
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPX3
BioGPS: 2878
Gene Expression Atlas: ENSG00000211445
The Human Protein Atlas: ENSG00000211445
PathwayNCI Pathway Interaction Database: GPX3
KEGG: GPX3
REACTOME: GPX3
ConsensusPathDB
Pathway Commons: GPX3
MetabolismMetaCyc: GPX3
HUMANCyc: GPX3
RegulationEnsembl's Regulation: ENSG00000211445
miRBase: chr5 :150,399,998-150,408,554
TargetScan: NM_002084
cisRED: ENSG00000211445
ContextiHOP: GPX3
cancer metabolism search in PubMed: GPX3
UCL Cancer Institute: GPX3
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GPX3 in cancer cell metabolism1. Lin HY, Kuo YC, Weng YI, Lai IL, Huang TH, et al. (2012) Activation of silenced tumor suppressor genes in prostate cancer cells by a novel energy restriction-mimetic agent. Prostate 72: 1767-1778. doi: 10.1002/pros.22530. pmid: 3867924. go to article
2. Morvan D, Demidem A (2014) Metabolomics and transcriptomics demonstrate severe oxidative stress in both localized chemotherapy-treated and bystander tumors. Biochim Biophys Acta 1840: 1092-1104. doi: 10.1016/j.bbagen.2013.11.022. go to article

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Phenotypic Information for GPX3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GPX3
Familial Cancer Database: GPX3
* 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
KEGG_ARACHIDONIC_ACID_METABOLISM

check002.gifOthers
OMIM 138321; gene.
Orphanet
DiseaseKEGG Disease: GPX3
MedGen: GPX3 (Human Medical Genetics with Condition)
ClinVar: GPX3
PhenotypeMGI: GPX3 (International Mouse Phenotyping Consortium)
PhenomicDB: GPX3

Mutations for GPX3
* 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 GPX3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CV421185GPX319865150408223150408290NSMCE186174162723845227238540
AA740310GPX312275150408293150408522RPN2219437203581258535826827
BG430541GPX312165150407618150407832GPX32124825150406467150407527
BF848871AARS26183167028765770287931GPX31784045150407985150408211
BG896291GPX3882315150407947150408090GPX32293865150408072150408229
BG927502GPX3853005150407777150407992GPX32965715150407030150407682
BF878552GPX312485150404982150407052GPX32393215150404898150404980
BF954117AARS26183167028765770287931GPX31784045150407985150408211
AW794509GPX312535150407731150407982S100A82434161153362669153362993
CB044109INPP4B1892434142963302142963356GPX32426725150406475150407696
BG990596AFAP1L2118010116056714116057013GPX31742815150406494150407015
W25873GPX3191195150407479150407578GPX31144635150407726150408075

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=14)
Stat. for Synonymous SNVs
(# total SNVs=1)
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
chr5:150407000-150407000p.R123G2
chr5:150407669-150407669p.A220V2
chr5:150400239-150400239p.S8S1
chr5:150407548-150407548p.R180S1
chr5:150400298-150400298p.S28L1
chr5:150407549-150407549p.R180H1
chr5:150404937-150404937p.E42K1
chr5:150407576-150407576p.G189V1
chr5:150404944-150404944p.G44E1
chr5:150407585-150407585p.G192D1

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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=0

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample                    
# mutation                    
nonsynonymous SNV                    
synonymous SNV                    
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

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 GPX3 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 GPX3

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

ADH1B,ADIPOQ,AOC3,AQP7,AQP7P1,C14orf180,CIDEC,
FABP4,G0S2,GPD1,GPX3,ITIH5,KCNIP2,LIPE,
LOC339524,NPR1,PLIN1,PLIN4,RDH5,SLC19A3,TMEM37
ANTXR2,CALCOCO2,CDKN2B,CYP4B1,DUSP22,FGFBP2,GABARAPL1,
GALNT15,GPX3,GTF2E2,LAMC1,MAOA,NDRG1,PRDX6,
PRELP,SH3D19,SH3KBP1,ST6GALNAC6,TIMP3,TIMP4,VIM

ABCA9,ACSM5,ADH1B,ADIPOQ,CD300LG,CD36,CIDEA,
FABP4,GLYAT,GPX3,HEPACAM,KCNIP2,LEP,LGALS12,
LOC339524,PLAC9,PLIN1,PLIN4,SCN4A,SEMA3G,TUSC5
ADAMTS2,AOX1,ARHGAP29,C1R,C1S,CACNB4,CLDN11,
CRLF1,CSRP2,EFEMP1,FAM198A,TMEM255A,GALNT15,GPX3,
IL1R1,SERPINF1,SPON2,STEAP4,TPST1,WISP2,WTIP
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 GPX3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA28951; -.
Organism-specific databasesCTD 2878; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00143glutathione peroxidase 3 (plasma)approved; nutraceuticalGlutathione
DB00515glutathione peroxidase 3 (plasma)approvedCisplatin


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Cross referenced IDs for GPX3
* 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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