Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolGSTA4
Gene nameglutathione S-transferase alpha 4
SynonymsGSTA4-4|GTA4
CytomapUCSC genome browser: 6p12.1
Genomic locationchr6 :52842745-52860178
Type of geneprotein-coding
RefGenesNM_001512.3,
Ensembl idENSG00000170899
DescriptionGST 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 date20141207
dbXrefs MIM : 605450
HGNC : HGNC
Ensembl : ENSG00000170899
HPRD : 06899
Vega : OTTHUMG00000014868
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GSTA4
BioGPS: 2941
Gene Expression Atlas: ENSG00000170899
The Human Protein Atlas: ENSG00000170899
PathwayNCI Pathway Interaction Database: GSTA4
KEGG: GSTA4
REACTOME: GSTA4
ConsensusPathDB
Pathway Commons: GSTA4
MetabolismMetaCyc: GSTA4
HUMANCyc: GSTA4
RegulationEnsembl's Regulation: ENSG00000170899
miRBase: chr6 :52,842,745-52,860,178
TargetScan: NM_001512
cisRED: ENSG00000170899
ContextiHOP: GSTA4
cancer metabolism search in PubMed: GSTA4
UCL Cancer Institute: GSTA4
Assigned class in ccmGDBC

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Phenotypic Information for GSTA4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_GLUTATHIONE_METABOLISM
KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450
KEGG_DRUG_METABOLISM_CYTOCHROME_P450

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GSTA4
MedGen: GSTA4 (Human Medical Genetics with Condition)
ClinVar: GSTA4
PhenotypeMGI: GSTA4 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryGSTA4chr65285732152857341chr65286168852861708
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GSTA4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BX477527LRRK117215101555467101555538GSTA46757065284983152850334

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr6:52850344-52850344p.E59D2
chr6:52843291-52843291p.V216I2
chr6:52849366-52849366p.E104K2
chr6:52852158-52852158p.D46Y2
chr6:52847488-52847488p.G144R2
chr6:52849319-52849319p.K119N1
chr6:52850345-52850345p.E59G1
chr6:52849324-52849324p.Q118*1
chr6:52850346-52850346p.E59K1
chr6:52843314-52843314p.P208fs*61

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample1   2 1    221   2 4
# mutation1   2 1    221   2 4
nonsynonymous SNV1   2      221   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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr6:52850269p.H49Y1
chr6:52843291p.D46Y1
chr6:52850330p.V216I1
chr6:52843315p.P208T1
chr6:52850344p.G201V1
chr6:52843335p.I174I1
chr6:52850346p.E169D1
chr6:52847396p.P134L1
chr6:52850376p.K119N1
chr6:52847411p.G98G1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00143glutathione S-transferase alpha 4approved; nutraceuticalGlutathione
DB00515glutathione S-transferase alpha 4approvedCisplatin
DB01248glutathione S-transferase alpha 4approved; investigationalDocetaxel


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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



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