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 GPX5
Basic gene info.Gene symbolGPX5
Gene nameglutathione peroxidase 5
SynonymsHEL-S-75p
CytomapUCSC genome browser: 6p22.1
Genomic locationchr6_cox_hap2 :15992-24932
Type of geneprotein-coding
RefGenesNM_001509.2,
NM_003996.3,
Ensembl idENSG00000224586
DescriptionEGLPGPx-5GSHPx-5epididymal androgen-related proteinepididymal secretory glutathione peroxidaseepididymis secretory sperm binding protein Li 75pepididymis-specific glutathione peroxidase-like protein
Modification date20141207
dbXrefs MIM : 603435
HGNC : HGNC
Ensembl : ENSG00000224586
HPRD : 11941
Vega : OTTHUMG00000016307
ProteinUniProt: O75715
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPX5
BioGPS: 2880
Gene Expression Atlas: ENSG00000224586
The Human Protein Atlas: ENSG00000224586
PathwayNCI Pathway Interaction Database: GPX5
KEGG: GPX5
REACTOME: GPX5
ConsensusPathDB
Pathway Commons: GPX5
MetabolismMetaCyc: GPX5
HUMANCyc: GPX5
RegulationEnsembl's Regulation: ENSG00000224586
miRBase: chr6_cox_hap2 :15,992-24,932
TargetScan: NM_001509
cisRED: ENSG00000224586
ContextiHOP: GPX5
cancer metabolism search in PubMed: GPX5
UCL Cancer Institute: GPX5
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GPX5 in cancer cell metabolism1. Li Y, Sun Z, Cunningham JM, Aubry MC, Wampfler JA, et al. (2011) Genetic variations in multiple drug action pathways and survival in advanced stage non-small cell lung cancer treated with chemotherapy. Clin Cancer Res 17: 3830-3840. doi: 10.1158/1078-0432.CCR-10-2877. pmid: 3124814. go to article

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Phenotypic Information for GPX5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GPX5
Familial Cancer Database: GPX5
* 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 GBM 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.sciencedirect.com/science/article/pii/S0092867413012087,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_GLUTATHIONE_METABOLISM
KEGG_ARACHIDONIC_ACID_METABOLISM

check002.gifOthers
OMIM 603435; gene.
Orphanet
DiseaseKEGG Disease: GPX5
MedGen: GPX5 (Human Medical Genetics with Condition)
ClinVar: GPX5
PhenotypeMGI: GPX5 (International Mouse Phenotyping Consortium)
PhenomicDB: GPX5

Mutations for GPX5
* 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 GPX5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=43)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr6:28497279-28497279p.A47T8
chr6:28501867-28501867p.R197C3
chr6:28499659-28499659p.L116F2
chr6:28501803-28501803p.K175N2
chr6:28497370-28497370p.A77V2
chr6:28499572-28499572p.E87K2
chr6:28501836-28501836p.F186F2
chr6:28499606-28499606p.G98D2
chr6:28501858-28501858p.P194S2
chr6:28501787-28501787p.S170F2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 74 1 1  62   121 6
# mutation 2 53 1 1  72   131 5
nonsynonymous SNV 2 53 1 1  62   91 5
synonymous SNV           1    4   
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
chr6:28501867p.A47T,GPX53
chr6:28497279p.R197C3
chr6:28493868p.E26D,GPX52
chr6:28499606p.L116I2
chr6:28499659p.K175N2
chr6:28501803p.G98D2
chr6:28493824p.P12S,GPX52
chr6:28497345p.V207V1
chr6:28501750p.M30I,GPX51
chr6:28493858p.Y121D1

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 GPX5 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 GPX5

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

C1QL4,C8orf46,CFAP58,CYP27C1,EFR3B,FLJ35024,GPX5,
KCNJ9,KIF2B,MAGEB1,OR10A6,OR7C2,PRSS38,PSORS1C3,
RPE65,SIX3,SLC17A1,SLC45A3,SPANXN1,TMEM61,USH2A
CDC6,CENPF,CENPI,CKAP2L,CYP4F8,E2F7,FMO6P,
GALNTL5,GPX5,IQGAP3,KIF14,KIF15,LOC440896,MKI67,
MMP3,PRG3,PRM3,PRR11,SPC24,TNFSF18,TOP2A

AMBN,CACNA1S,CALML3,CST5,DBH,FGF8,GPX5,
KLK14,KRT31,LIPM,LOC144742,NELL2,OR4C3,PNMT,
RPTN,S100A3,SERPINI1,SEZ6L,TCHHL1,TDRD12,TULP2
ACAN,AWAT2,ADM5,C20orf141,NCOR1P1,BPIFA2,CHAT,
CLEC4G,GPX5,ITIH3,KPRP,LCE2C,LPA,MEPE,
CHODL-AS1,OBP2A,OR2D2,PGLYRP3,SNORA79,TRIM6-TRIM34,ZSWIM2
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 GPX5
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA28953; -.
Organism-specific databasesCTD 2880; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00143glutathione peroxidase 5 (epididymal androgen-related protein)approved; nutraceuticalGlutathione
DB00515glutathione peroxidase 5 (epididymal androgen-related protein)approvedCisplatin


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Cross referenced IDs for GPX5
* 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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