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 GPX1
Basic gene info.Gene symbolGPX1
Gene nameglutathione peroxidase 1
SynonymsGPXD|GSHPX1
CytomapUCSC genome browser: 3p21.3
Genomic locationchr3 :49394608-49395791
Type of geneprotein-coding
RefGenesNM_000581.2,
NM_201397.1,
Ensembl idENSG00000233276
DescriptionGPx-1GSHPx-1cellular glutathione peroxidase
Modification date20141222
dbXrefs MIM : 138320
HGNC : HGNC
Ensembl : ENSG00000233276
HPRD : 11749
Vega : OTTHUMG00000156837
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPX1
BioGPS: 2876
Gene Expression Atlas: ENSG00000233276
The Human Protein Atlas: ENSG00000233276
PathwayNCI Pathway Interaction Database: GPX1
KEGG: GPX1
REACTOME: GPX1
ConsensusPathDB
Pathway Commons: GPX1
MetabolismMetaCyc: GPX1
HUMANCyc: GPX1
RegulationEnsembl's Regulation: ENSG00000233276
miRBase: chr3 :49,394,608-49,395,791
TargetScan: NM_000581
cisRED: ENSG00000233276
ContextiHOP: GPX1
cancer metabolism search in PubMed: GPX1
UCL Cancer Institute: GPX1
Assigned class in ccmGDBC

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Phenotypic Information for GPX1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GPX1
Familial Cancer Database: GPX1
* 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
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PURINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GPX1
MedGen: GPX1 (Human Medical Genetics with Condition)
ClinVar: GPX1
PhenotypeMGI: GPX1 (International Mouse Phenotyping Consortium)
PhenomicDB: GPX1

Mutations for GPX1
* 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 GPX1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP429026GPX1729234939492549395489RPL3291388223970970339710177
AA995621GPX11615934939460949394752SLC35B3150315684354348435599

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=11

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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=2)
Stat. for Deletions
(# total SNVs=1)		Stat. for Insertions
(# total SNVs=1)

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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
chr3:49395482-49395482p.P77R11
chr3:49395688-49395688p.A8A1
chr3:49395053-49395053p.A127V1
chr3:49395694-49395694p.L6L1
chr3:49395068-49395069p.A122fs*441
chr3:49395695-49395695p.L6R1
chr3:49395097-49395097p.F112L1
chr3:49394857-49394857p.I192I1
chr3:49395100-49395100p.L111L1
chr3:49394909-49394909p.P175L1

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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 GPX1 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 GPX1

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

APOE,ARL6IP4,AURKAIP1,BCL7C,C19orf24,C19orf60,C1orf86,
LAMTOR4,C9orf16,CCDC12,CCM2,GPX1,NDUFA11,NDUFS7,
OAZ1,INAFM1,RPS19BP1,THAP3,TWF2,UQCR11,ZNHIT1		ANXA11,ARL2,CCDC107,CCM2,CD151,CD63,CD81,
GPX1,GPX4,ITFG3,LGALS1,LRP3,MYL6,NAGLU,
NME4,NUCB1,POLR2L,PRR5,RNPEPL1,SNX17,UROD

ASNA1,C11orf31,ELP6,FAU,GADD45GIP1,GEMIN7,GPX1,
GSTO1,MED31,MRPL43,MRPL54,MYEOV2,NDUFA11,NDUFA13,
NDUFA2,NDUFB7,PFDN5,RPSA,RPSAP58,TIMM8B,UQCR11		ADSL,ANAPC11,ASNA1,C19orf53,ATRAID,GPX1,HAX1,
HSCB,MRPL57,MRPL43,MRPL54,NDUFA11,NDUFA7,POP7,
RPL27A,RPL35,RPS10,RPS14,SNRPD2,STOML2,ZNF511
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 GPX1
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
DB00143glutathione peroxidase 1approved; nutraceuticalGlutathione
DB01694glutathione peroxidase 1experimentalD-tartaric acid
DB01942glutathione peroxidase 1experimentalFormic Acid
DB01975glutathione peroxidase 1experimentalAMPCPR
DB02059glutathione peroxidase 1experimentalAdenosine-5-Diphosphoribose
DB03148glutathione peroxidase 1experimentalPhosphomethylphosphonic Acid Adenosyl Ester
DB01992glutathione peroxidase 1experimentalCoenzyme A
DB03014glutathione peroxidase 1experimentalHeme
DB03766glutathione peroxidase 1experimentalPropanoic Acid
DB03247glutathione peroxidase 1experimentalRiboflavin Monophosphate
DB03382glutathione peroxidase 1experimentalS-Oxy Cysteine
DB03661glutathione peroxidase 1experimentalCysteinesulfonic Acid
DB04580glutathione peroxidase 1experimental1-Methyl-2-quinolone
DB04605glutathione peroxidase 1experimental5-Aminoisoquinoline
DB00515glutathione peroxidase 1approvedCisplatin
DB00171glutathione peroxidase 1approved; nutraceuticalAdenosine triphosphate
DB01205glutathione peroxidase 1approvedFlumazenil
DB00997glutathione peroxidase 1approved; investigationalDoxorubicin
DB00783glutathione peroxidase 1approved; investigationalEstradiol
DB00675glutathione peroxidase 1approvedTamoxifen


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Cross referenced IDs for GPX1
* 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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