Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	GPX3
	Gene name	glutathione peroxidase 3 (plasma)
	Synonyms	GPx-P\|GSHPx-3\|GSHPx-P
	Cytomap	UCSC genome browser: 5q23
	Genomic location	chr5 :150399998-150408554
	Type of gene	protein-coding
	RefGenes	NM_002084.3,
	Ensembl id	ENSG00000211445
	Description	GPx-3extracellular glutathione peroxidaseglutathione peroxidase 3plasma glutathione peroxidase
	Modification date	20141222
dbXrefs	MIM : 138321
	HGNC : HGNC
	Ensembl : ENSG00000211445
	HPRD : 11750
	Vega : OTTHUMG00000163693
Protein	UniProt: P22352 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GPX3
	BioGPS: 2878
	Gene Expression Atlas: ENSG00000211445
	The Human Protein Atlas: ENSG00000211445
Pathway	NCI Pathway Interaction Database: GPX3
	KEGG: GPX3
	REACTOME: GPX3
	ConsensusPathDB
	Pathway Commons: GPX3
Metabolism	MetaCyc: GPX3
	HUMANCyc: GPX3
Regulation	Ensembl's Regulation: ENSG00000211445
	miRBase: chr5 :150,399,998-150,408,554
	TargetScan: NM_002084
	cisRED: ENSG00000211445
Context	iHOP: GPX3
	cancer metabolism search in PubMed: GPX3
	UCL Cancer Institute: GPX3
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GPX3 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_GLUTATHIONE_METABOLISM KEGG_ARACHIDONIC_ACID_METABOLISM

Others
OMIM	138321; gene.
Orphanet
Disease	KEGG Disease: GPX3
	MedGen: GPX3 (Human Medical Genetics with Condition)
	ClinVar: GPX3
Phenotype	MGI: GPX3 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GPX3 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
CV421185	GPX3	19	86	5	150408223	150408290	NSMCE1	86	174	16	27238452	27238540
AA740310	GPX3	1	227	5	150408293	150408522	RPN2	219	437	20	35812585	35826827
BG430541	GPX3	1	216	5	150407618	150407832	GPX3	212	482	5	150406467	150407527
BF848871	AARS	26	183	16	70287657	70287931	GPX3	178	404	5	150407985	150408211
BG896291	GPX3	88	231	5	150407947	150408090	GPX3	229	386	5	150408072	150408229
BG927502	GPX3	85	300	5	150407777	150407992	GPX3	296	571	5	150407030	150407682
BF878552	GPX3	1	248	5	150404982	150407052	GPX3	239	321	5	150404898	150404980
BF954117	AARS	26	183	16	70287657	70287931	GPX3	178	404	5	150407985	150408211
AW794509	GPX3	1	253	5	150407731	150407982	S100A8	243	416	1	153362669	153362993
CB044109	INPP4B	189	243	4	142963302	142963356	GPX3	242	672	5	150406475	150407696
BG990596	AFAP1L2	1	180	10	116056714	116057013	GPX3	174	281	5	150406494	150407015
W25873	GPX3	19	119	5	150407479	150407578	GPX3	114	463	5	150407726	150408075

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr5:150407000-150407000	p.R123G	2
chr5:150407669-150407669	p.A220V	2
chr5:150405018-150405018	p.V69M	1
chr5:150407589-150407589	p.I193M	1
chr5:150406496-150406496	p.G93S	1
chr5:150407602-150407602	p.W198G	1
chr5:150406533-150406533	p.G105E	1
chr5:150407618-150407618	p.T203M	1
chr5:150407641-150407641	p.I211V	1
chr5:150407039-150407039	p.E136Q	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# 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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Top 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 Position

Mutation(aa)

Unique sampleID count

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA28951; -.
Organism-specific databases	CTD	2878; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00143	glutathione peroxidase 3 (plasma)	approved; nutraceutical	Glutathione
DB00515	glutathione peroxidase 3 (plasma)	approved	Cisplatin

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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