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 GPX5

Basic gene info.	Gene symbol	GPX5
	Gene name	glutathione peroxidase 5
	Synonyms	HEL-S-75p
	Cytomap	UCSC genome browser: 6p22.1
	Genomic location	chr6_cox_hap2 :15992-24932
	Type of gene	protein-coding
	RefGenes	NM_001509.2, NM_003996.3,
	Ensembl id	ENSG00000224586
	Description	EGLPGPx-5GSHPx-5epididymal androgen-related proteinepididymal secretory glutathione peroxidaseepididymis secretory sperm binding protein Li 75pepididymis-specific glutathione peroxidase-like protein
	Modification date	20141207
dbXrefs	MIM : 603435
	HGNC : HGNC
	Ensembl : ENSG00000224586
	HPRD : 11941
	Vega : OTTHUMG00000016307
Protein	UniProt: O75715 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GPX5
	BioGPS: 2880
	Gene Expression Atlas: ENSG00000224586
	The Human Protein Atlas: ENSG00000224586
Pathway	NCI Pathway Interaction Database: GPX5
	KEGG: GPX5
	REACTOME: GPX5
	ConsensusPathDB
	Pathway Commons: GPX5
Metabolism	MetaCyc: GPX5
	HUMANCyc: GPX5
Regulation	Ensembl's Regulation: ENSG00000224586
	miRBase: chr6_cox_hap2 :15,992-24,932
	TargetScan: NM_001509
	cisRED: ENSG00000224586
Context	iHOP: GPX5
	cancer metabolism search in PubMed: GPX5
	UCL Cancer Institute: GPX5
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GPX5 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_GLUTATHIONE_METABOLISM KEGG_ARACHIDONIC_ACID_METABOLISM

Others
OMIM	603435; gene.
Orphanet
Disease	KEGG Disease: GPX5
	MedGen: GPX5 (Human Medical Genetics with Condition)
	ClinVar: GPX5
Phenotype	MGI: GPX5 (International Mouse Phenotyping Consortium)
Phenotype	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.

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 GPX5 related fusion information.

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

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=8

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Somatic 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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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
chr6:28497279-28497279	p.A47T	8
chr6:28501867-28501867	p.R197C	3
chr6:28501803-28501803	p.K175N	2
chr6:28497370-28497370	p.A77V	2
chr6:28499572-28499572	p.E87K	2
chr6:28501836-28501836	p.F186F	2
chr6:28499606-28499606	p.G98D	2
chr6:28501858-28501858	p.P194S	2
chr6:28501787-28501787	p.S170F	2
chr6:28493824-28493824	p.P12S	2

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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=3

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		2		7	4		1		1			6	2				12	1		6
# mutation		2		5	3		1		1			7	2				13	1		5
nonsynonymous SNV		2		5	3		1		1			6	2				9	1		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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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
chr6:28497279	p.R197C	3
chr6:28501867	p.A47T,GPX5	3
chr6:28499606	p.K175N	2
chr6:28499659	p.G98D	2
chr6:28501803	p.P12S,GPX5	2
chr6:28493824	p.L116I	2
chr6:28493868	p.E26D,GPX5	2
chr6:28497230	p.S55F,GPX5	1
chr6:28499572	p.K147T	1
chr6:28501767	p.H63Y,GPX5	1

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 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

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


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

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 GPX5

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA28953; -.
Organism-specific databases	CTD	2880; -.

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 5 (epididymal androgen-related protein)	approved; nutraceutical	Glutathione
DB00515	glutathione peroxidase 5 (epididymal androgen-related protein)	approved	Cisplatin

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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