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 GPX7
Basic gene info.Gene symbolGPX7
Gene nameglutathione peroxidase 7
SynonymsCL683|GPX6|GPx-7|GSHPx-7|NPGPx
CytomapUCSC genome browser: 1p32
Genomic locationchr1 :53068042-53074723
Type of geneprotein-coding
RefGenesNM_015696.4,
Ensembl idENSG00000116157
Descriptionglutathione peroxidase 6non-selenocysteine containing phospholipid hydroperoxide glutathione peroxidase
Modification date20141207
dbXrefs MIM : 615784
HGNC : HGNC
Ensembl : ENSG00000116157
HPRD : 13606
Vega : OTTHUMG00000008322
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPX7
BioGPS: 2882
Gene Expression Atlas: ENSG00000116157
The Human Protein Atlas: ENSG00000116157
PathwayNCI Pathway Interaction Database: GPX7
KEGG: GPX7
REACTOME: GPX7
ConsensusPathDB
Pathway Commons: GPX7
MetabolismMetaCyc: GPX7
HUMANCyc: GPX7
RegulationEnsembl's Regulation: ENSG00000116157
miRBase: chr1 :53,068,042-53,074,723
TargetScan: NM_015696
cisRED: ENSG00000116157
ContextiHOP: GPX7
cancer metabolism search in PubMed: GPX7
UCL Cancer Institute: GPX7
Assigned class in ccmGDBC

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Phenotypic Information for GPX7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GPX7
Familial Cancer Database: GPX7
* 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
Orphanet
DiseaseKEGG Disease: GPX7
MedGen: GPX7 (Human Medical Genetics with Condition)
ClinVar: GPX7
PhenotypeMGI: GPX7 (International Mouse Phenotyping Consortium)
PhenomicDB: GPX7

Mutations for GPX7
* 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 GPX7 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CV329033GPX7128915307242853074032CTGF2813766132270038132270134
CV329008GPX7128915307242853074032CTGF2813766132270038132270134

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=8)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=2)
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
chr1:53072531-53072531p.R105L2
chr1:53072383-53072383p.E56*2
chr1:53073950-53073950p.E139D2
chr1:53068088-53068088p.A3S2
chr1:53068093-53068093p.A4A2
chr1:53072504-53072504p.S96T1
chr1:53068137-53068137p.A19V1
chr1:53072522-53072522p.S102N1
chr1:53068149-53068149p.Q23fs*291
chr1:53072527-53072528p.R105fs*121

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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 1 1    1  31   23 3
# mutation 1 1    1  31   23 3
nonsynonymous SNV 1 1    1  3     3 1
synonymous SNV            1   2  2
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
chr1:53073967p.S55S1
chr1:53072382p.Q69R1
chr1:53073986p.N80N1
chr1:53072423p.G90G1
chr1:53074041p.S102C1
chr1:53072457p.S102N1
chr1:53072487p.R105H1
chr1:53072521p.R106S1
chr1:53072522p.T121T1
chr1:53072531p.E139K1

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 GPX7 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 GPX7

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

APBA2,BCL11A,CDK2AP1,CLIP2,DZIP1,FAM171A1,FBLIM1,
FHL3,GPX7,KDELC1,LDHB,MAGOH,MFAP2,OLFM2,
RGMA,SERPINH1,SRSF12,SMO,TMEM39B,UBE2E3,UQCRH
FAM216A,CDK4,CGREF1,CRABP1,FAM57A,FKBP10,FSCN1,
GPX7,KCNMB4,NPM3,NT5DC2,OSTC,PDE9A,RPLP0,
RPS2,RPSAP58,S1PR2,SMO,STMN1,TSPAN33,XPNPEP1

CERCAM,CMTM3,CNRIP1,CTSK,DCN,EFEMP2,EFS,
FKBP7,FSTL1,GPX7,IGFBP7,LGALS1,LUM,MAGEH1,
PCOLCE,PRRX1,RAB31,RAB34,SDC2,SPARC,THY1
AP1S2,BLVRA,DNAJC18,DUSP22,FAHD2B,GNB5,GPX7,
IGFBP7,LOC653653,MAGED2,MAGEH1,NRSN2,OAZ2,PKIA,
PRKD3,RAB34,RPL23AP82,RPS2P32,SELM,SMARCD3,TMEM55A
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 GPX7
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 7approved; nutraceuticalGlutathione
DB00515glutathione peroxidase 7approvedCisplatin


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Cross referenced IDs for GPX7
* 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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