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 GSTA4

Basic gene info.	Gene symbol	GSTA4
	Gene name	glutathione S-transferase alpha 4
	Synonyms	GSTA4-4\|GTA4
	Cytomap	UCSC genome browser: 6p12.1
	Genomic location	chr6 :52842745-52860178
	Type of gene	protein-coding
	RefGenes	NM_001512.3,
	Ensembl id	ENSG00000170899
	Description	GST class-alpha member 4S-(hydroxyalkyl)glutathione lyase A4glutathione S-alkyltransferase A4glutathione S-aralkyltransferase A4glutathione S-aryltransferase A4glutathione S-transferase A4glutathione S-transferase A4-4glutathione transferase A4-4
	Modification date	20141207
dbXrefs	MIM : 605450
	HGNC : HGNC
	Ensembl : ENSG00000170899
	HPRD : 06899
	Vega : OTTHUMG00000014868
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GSTA4
	BioGPS: 2941
	Gene Expression Atlas: ENSG00000170899
	The Human Protein Atlas: ENSG00000170899
Pathway	NCI Pathway Interaction Database: GSTA4
	KEGG: GSTA4
	REACTOME: GSTA4
	ConsensusPathDB
	Pathway Commons: GSTA4
Metabolism	MetaCyc: GSTA4
	HUMANCyc: GSTA4
Regulation	Ensembl's Regulation: ENSG00000170899
	miRBase: chr6 :52,842,745-52,860,178
	TargetScan: NM_001512
	cisRED: ENSG00000170899
Context	iHOP: GSTA4
	cancer metabolism search in PubMed: GSTA4
	UCL Cancer Institute: GSTA4
Assigned class in ccmGDB	C

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Phenotypic Information for GSTA4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GSTA4
	Familial Cancer Database: GSTA4

* 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
Orphanet
Disease	KEGG Disease: GSTA4
	MedGen: GSTA4 (Human Medical Genetics with Condition)
	ClinVar: GSTA4
Phenotype	MGI: GSTA4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GSTA4

Mutations for GSTA4

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	GSTA4	chr6	52857321	52857341		chr6	52861688	52861708

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GSTA4 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

BX477527

LRRK1

101555467

101555538

GSTA4

570

52849831

52850334

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=22)	Stat. for Synonymous SNVs (# total SNVs=0)
	There's no s-snv.
Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr6:52849366-52849366	p.E104K	2
chr6:52852158-52852158	p.D46Y	2
chr6:52847488-52847488	p.G144R	2
chr6:52850344-52850344	p.E59D	2
chr6:52843291-52843291	p.V216I	2
chr6:52849353-52849353	p.M108K	1
chr6:52850376-52850376	p.H49Y	1
chr6:52843335-52843335	p.G201V	1
chr6:52843336-52843336	p.G201C	1
chr6:52849383-52849383	p.G98E	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				2		1					2	2	1				2		4
# mutation	1				2		1					2	2	1				2		4
nonsynonymous SNV	1				2							2	2	1				1		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
chr6:52850344	p.P208T	1
chr6:52843335	p.G201V	1
chr6:52850346	p.I174I	1
chr6:52847396	p.E169D	1
chr6:52850376	p.P134L	1
chr6:52847411	p.K119N	1
chr6:52852158	p.G98G	1
chr6:52849275	p.E97D	1
chr6:52849319	p.Y95H	1
chr6:52849382	p.K84N	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 GSTA4 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 GSTA4

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


CCT6A,CHIA,DECR1,GSTA1,GSTA4,GTPBP2,ICK, KLHDC3,LOC340508,LOC730101,MRPS17,PHGDH,PHKG1,PPP2R5D, PROK1,PSPH,SEC61G,TAF11,TMEM14A,WFIKKN2,XPO5	C11orf1,C18orf21,CAMKMT,CAMLG,DPH5,EIF2S3,EIF3E, EIF3M,GSTA4,METAP2,NAP1L1,LRRC75A-AS1,PCBP2,PFDN4, PMPCB,POLR1D,RPS13,RPS29,SPATA7,TATDN1,TIMM9

C9orf66,CBY1,CPE,CREB3L4,DPPA3,GPR37L1,GSTA4, GSTTP2,HSPA2,IGFBP2,ITLN1,ITLN2,KLK12,LYZL6, MAPK15,GRIK1-AS1,RASD2,SHISA3,SLAIN1,T,UGT2B4	ASPH,BCAP29,BRMS1L,C10orf35,TMEM263,CFAP36,CDH19, DYNC1LI1,LINC01184,GSTA4,IL33,KIAA0895,LOH12CR2,MNAT1, NFYB,NME4,NME5,REXO2,SRR,TCEAL1,TCEAL8

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 GSTA4

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 alpha 4	approved; nutraceutical	Glutathione
DB00515	glutathione S-transferase alpha 4	approved	Cisplatin
DB01248	glutathione S-transferase alpha 4	approved; investigational	Docetaxel

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Cross referenced IDs for GSTA4

* 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