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 GSTT1

Basic gene info.	Gene symbol	GSTT1
	Gene name	glutathione S-transferase theta 1
	Synonyms	-
	Cytomap	UCSC genome browser: 22q11.23
	Genomic location	chr22 :24376138-24384284
	Type of gene	protein-coding
	RefGenes	NM_000853.3, NM_001293807.1,NM_001293808.1,NM_001293809.1,NM_001293810.1, NM_001293811.1,NM_001293812.1,NM_001293813.1,NM_001293814.1,
	Ensembl id	ENSG00000184674
	Description	GST class-theta-1glutathione S-transferase theta-1glutathione transferase T1-1
	Modification date	20141222
dbXrefs	MIM : 600436
	HGNC : HGNC
	HPRD : 02700
Protein	UniProt: P30711 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GSTT1
	BioGPS: 2952
	Gene Expression Atlas: ENSG00000184674
	The Human Protein Atlas: ENSG00000184674
Pathway	NCI Pathway Interaction Database: GSTT1
	KEGG: GSTT1
	REACTOME: GSTT1
	ConsensusPathDB
	Pathway Commons: GSTT1
Metabolism	MetaCyc: GSTT1
	HUMANCyc: GSTT1
Regulation	Ensembl's Regulation: ENSG00000184674
	miRBase: chr22 :24,376,138-24,384,284
	TargetScan: NM_000853
	cisRED: ENSG00000184674
Context	iHOP: GSTT1
	cancer metabolism search in PubMed: GSTT1
	UCL Cancer Institute: GSTT1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for GSTT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GSTT1
	Familial Cancer Database: GSTT1

* 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_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 KEGG_DRUG_METABOLISM_CYTOCHROME_P450

Others
OMIM	600436; gene.
Orphanet
Disease	KEGG Disease: GSTT1
	MedGen: GSTT1 (Human Medical Genetics with Condition)
	ClinVar: GSTT1
Phenotype	MGI: GSTT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GSTT1

Mutations for GSTT1

* 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 GSTT1 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

CN352897

GSTT1

111

24384119

24384230

SLC2A11

108

398

24217301

24224677

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=8)	Stat. for Synonymous SNVs (# total SNVs=3)

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
chr22:24376512-24376512	p.E212K	1
chr22:24384148-24384148	p.F28L	1
chr22:24376534-24376534	p.E204E	1
chr22:24384187-24384187	p.R15R	1
chr22:24376834-24376834	p.T172T	1
chr22:24384206-24384206	p.L9Q	1
chr22:24376835-24376835	p.T172M	1
chr22:24384213-24384213	p.L7L	1
chr22:24376836-24376836	p.T172A	1
chr22:24384222-24384222	p.E4Q	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	2	1	1	3			1			1				1		2	2	2		1
# mutation	2	1	1	4			1			1				1		2	2	2		1
nonsynonymous SNV		1	1	2			1			1						1	2	2		1
synonymous SNV	2			2										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
chr22:24381723	p.R96W	2
chr22:24376534	p.T54M,GSTT1	1
chr22:24384213	p.T54A,GSTT1	1
chr22:24376834	p.S46S,GSTT1	1
chr22:24384222	p.S11F,GSTT1	1
chr22:24376835	p.L71P	1
chr22:24384226	p.F28L,GSTT1	1
chr22:24376836	p.Y18H,GSTT1	1
chr22:24384228	p.R15R,GSTT1	1
chr22:24376858	p.L7L,GSTT1	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 GSTT1 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 GSTT1

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


ALKBH7,SMDT1,CCDC157,CHCHD5,CIRBP,COQ4,DGCR6L, DENND6B,FBXW4,GSTT1,HSCB,LOC391322,MRPL54,RAB17, RHBDD3,RNF215,THAP7,TMEM205,TXN2,TXNRD2,WBP1	APLNR,ATG9A,NATD1,C1QTNF9,LINC00310,C22orf39,C6orf106, TMEM246,MICU1,CDH13,GSTT1,H19,HOXA10,LINC00652, KLHL30,LOC391322,PDE4A,ST3GAL3,SYNPO,UBE2D4,ZAK

ACY3,ALDH3A2,APOBEC1,ASL,B3GALT5,BTNL8,C1orf210, MICU1,CIB1,CLDN7,CTSE,CYP2C18,GSTT1,LIMA1, PIGR,PLA2G10,SDCBP2,SLC41A2,SULT1C2,TSPAN1,ZNF488	BCORP1,DNAAF2,CD9,CRYM,DCAF4,DDX43,ERI3, EXOSC4,FAM162A,GGH,GSTT1,HAS2-AS1,DANCR,LCN15, LOC100128822,LOC391322,RPS4Y2,TP53RK,TTTY10,ZNF544,ZNF702P

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 GSTT1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL2141; -.
Organism-specific databases	PharmGKB	PA183; -.
Organism-specific databases	CTD	2952; -.

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 theta 1	approved; nutraceutical	Glutathione
DB01234	glutathione S-transferase theta 1	approved; investigational	Dexamethasone
DB00650	glutathione S-transferase theta 1	approved	Leucovorin
DB00997	glutathione S-transferase theta 1	approved; investigational	Doxorubicin
DB04572	glutathione S-transferase theta 1	approved	Thiotepa
DB00412	glutathione S-transferase theta 1	approved; investigational	Rosiglitazone
DB00958	glutathione S-transferase theta 1	approved	Carboplatin
DB01181	glutathione S-transferase theta 1	approved	Ifosfamide
DB00526	glutathione S-transferase theta 1	approved; investigational	Oxaliplatin
DB00445	glutathione S-transferase theta 1	approved	Epirubicin
DB00515	glutathione S-transferase theta 1	approved	Cisplatin
DB00531	glutathione S-transferase theta 1	approved; investigational	Cyclophosphamide
DB00544	glutathione S-transferase theta 1	approved	Fluorouracil
DB00444	glutathione S-transferase theta 1	approved	Teniposide
DB01042	glutathione S-transferase theta 1	approved	Melphalan
DB00564	glutathione S-transferase theta 1	approved; investigational	Carbamazepine
DB00987	glutathione S-transferase theta 1	approved; investigational	Cytarabine
DB00694	glutathione S-transferase theta 1	approved	Daunorubicin
DB00773	glutathione S-transferase theta 1	approved	Etoposide
DB01033	glutathione S-transferase theta 1	approved	Mercaptopurine
DB00563	glutathione S-transferase theta 1	approved	Methotrexate
DB00635	glutathione S-transferase theta 1	approved	Prednisone
DB00541	glutathione S-transferase theta 1	approved; investigational	Vincristine
DB01008	glutathione S-transferase theta 1	approved; investigational	Busulfan
DB01101	glutathione S-transferase theta 1	approved; investigational	Capecitabine
DB00762	glutathione S-transferase theta 1	approved; investigational	Irinotecan
DB00382	glutathione S-transferase theta 1	approved	Tacrine
DB01060	glutathione S-transferase theta 1	approved	Amoxicillin
DB00766	glutathione S-transferase theta 1	approved	Clavulanate
DB00951	glutathione S-transferase theta 1	approved	Isoniazid
DB00197	glutathione S-transferase theta 1	withdrawn	Troglitazone

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Cross referenced IDs for GSTT1

* 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