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 GSTZ1

Basic gene info.	Gene symbol	GSTZ1
	Gene name	glutathione S-transferase zeta 1
	Synonyms	GSTZ1-1\|MAAI\|MAI
	Cytomap	UCSC genome browser: 14q24.3
	Genomic location	chr14 :77787705-77797940
	Type of gene	protein-coding
	RefGenes	NM_001513.3, NM_145870.2,NM_145871.2,
	Ensembl id	ENSG00000100577
	Description	S-(hydroxyalkyl)glutathione lyaseglutathione S-alkyltransferaseglutathione S-aralkyltransferaseglutathione S-aryltransferaseglutathione transferase zeta 1maleylacetoacetate isomerasemaleylacetone isomerase
	Modification date	20141207
dbXrefs	MIM : 603758
	HGNC : HGNC
	Ensembl : ENSG00000100577
	HPRD : 04785
	Vega : OTTHUMG00000171551
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GSTZ1
	BioGPS: 2954
	Gene Expression Atlas: ENSG00000100577
	The Human Protein Atlas: ENSG00000100577
Pathway	NCI Pathway Interaction Database: GSTZ1
	KEGG: GSTZ1
	REACTOME: GSTZ1
	ConsensusPathDB
	Pathway Commons: GSTZ1
Metabolism	MetaCyc: GSTZ1
	HUMANCyc: GSTZ1
Regulation	Ensembl's Regulation: ENSG00000100577
	miRBase: chr14 :77,787,705-77,797,940
	TargetScan: NM_001513
	cisRED: ENSG00000100577
Context	iHOP: GSTZ1
	cancer metabolism search in PubMed: GSTZ1
	UCL Cancer Institute: GSTZ1
Assigned class in ccmGDB	C

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Phenotypic Information for GSTZ1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GSTZ1
	Familial Cancer Database: GSTZ1

* 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_TYROSINE_METABOLISM KEGG_GLUTATHIONE_METABOLISM KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 KEGG_DRUG_METABOLISM_CYTOCHROME_P450 REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM
Orphanet
Disease	KEGG Disease: GSTZ1
	MedGen: GSTZ1 (Human Medical Genetics with Condition)
	ClinVar: GSTZ1
Phenotype	MGI: GSTZ1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GSTZ1

Mutations for GSTZ1

* 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 GSTZ1 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
BM833317	PCBD2	1	54	5	134260240	134260294	GSTZ1	50	441	14	77791211	77795526
BM820517	PCBD2	1	56	5	134260240	134260295	GSTZ1	52	609	14	77791211	77797458
AI636936	ADAP2	1	309	17	29284924	29285233	GSTZ1	309	431	14	77787427	77791235

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=9)	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
chr14:77796116-77796116	p.Q92R	1
chr14:77796651-77796651	p.?	1
chr14:77794294-77794294	p.P31S	1
chr14:77796689-77796689	p.A116T	1
chr14:77794296-77794296	p.P31P	1
chr14:77797425-77797425	p.L125I	1
chr14:77794333-77794333	p.V44M	1
chr14:77797454-77797454	p.I134M	1
chr14:77794336-77794336	p.R45C	1
chr14:77797487-77797487	p.Q145H	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=2

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	1	1		3								1	2				1	2		5
# mutation	1	1		3								1	2				1	3		5
nonsynonymous SNV	1	1		3								1	2					3		4
synonymous SNV																	1			1

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
chr14:77795519	p.Q90H,GSTZ1	2
chr14:77794333	p.P86P,GSTZ1	1
chr14:77794336	p.V99M,GSTZ1	1
chr14:77791214	p.R100C,GSTZ1	1
chr14:77795495	p.E82E,GSTZ1	1
chr14:77791217	p.Q105R,GSTZ1	1
chr14:77791255	p.A129T,GSTZ1	1
chr14:77796116	p.I147M,GSTZ1	1
chr14:77791264	p.P6L,GSTZ1	1
chr14:77796689	p.Q158H,GSTZ1	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 GSTZ1 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 GSTZ1

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


ACAA1,SLIRP,IFT43,C14orf2,CHCHD5,COQ4,COQ6, DCXR,DHRS4,DHRS4L2,EDF1,ENDOG,GSTZ1,ISCA2, MRPL41,MRPL54,NDUFB1,SDSL,TEX264,TP53TG1,WDR25	ADCK2,APEH,CDK5,COQ4,DDRGK1,DUS1L,EIF3I, GCAT,GSS,GSTZ1,MCAT,MLST8,MRPS34,NUDT16L1, RUVBL2,STK16,STRA13,TIMM13,TMEM141,TRUB2,TUFM

SLIRP,C14orf2,C14orf80,CINP,COQ4,COQ6,DHRS4, DHRS4L2,DLST,EMC9,GLRX5,GSTZ1,MED11,MRPL27, NUDT8,OSGEP,PLEK2,PSMB5,PSMC1,RPL36AL,VTI1B	ARL6IP1,ATPIF1,MPC2,PTRHD1,COQ4,COX4I1,COX5A, COX6A1,COX8A,GSTK1,GSTZ1,HARBI1,KTI12,LSM4, MTCH2,PDSS1,RAB25,TIMM13,TP53I3,TSPAN17,UQCRC1

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 GSTZ1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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 S-transferase zeta 1	approved; nutraceutical	Glutathione
DB04447	glutathione S-transferase zeta 1	experimental	1,4-Dithiothreitol
DB00515	glutathione S-transferase zeta 1	approved	Cisplatin
DB00120	glutathione S-transferase zeta 1	approved; nutraceutical	L-Phenylalanine
DB00135	glutathione S-transferase zeta 1	approved; nutraceutical	L-Tyrosine
DB00360	glutathione S-transferase zeta 1	approved; investigational	Tetrahydrobiopterin

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Cross referenced IDs for GSTZ1

* 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