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 GGT1
Basic gene info.Gene symbolGGT1
Gene namegamma-glutamyltransferase 1
SynonymsCD224|D22S672|D22S732|GGT|GGT 1|GTG
CytomapUCSC genome browser: 22q11.23
Genomic locationchr22 :24999123-25024972
Type of geneprotein-coding
RefGenesNM_013421.2,
NM_013430.2,NM_001032364.2,NM_001032365.2,NM_005265.3,
NM_001288833.1,
Ensembl idENSG00000100031
Descriptiongamma-glutamyltranspeptidase 1glutathione hydrolase 1leukotriene-C4 hydrolase
Modification date20141215
dbXrefs MIM : 612346
HGNC : HGNC
Ensembl : ENSG00000100031
HPRD : 01980
Vega : OTTHUMG00000030859
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GGT1
BioGPS: 2678
Gene Expression Atlas: ENSG00000100031
The Human Protein Atlas: ENSG00000100031
PathwayNCI Pathway Interaction Database: GGT1
KEGG: GGT1
REACTOME: GGT1
ConsensusPathDB
Pathway Commons: GGT1
MetabolismMetaCyc: GGT1
HUMANCyc: GGT1
RegulationEnsembl's Regulation: ENSG00000100031
miRBase: chr22 :24,999,123-25,024,972
TargetScan: NM_013421
cisRED: ENSG00000100031
ContextiHOP: GGT1
cancer metabolism search in PubMed: GGT1
UCL Cancer Institute: GGT1
Assigned class in ccmGDBC

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Phenotypic Information for GGT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GGT1
Familial Cancer Database: GGT1
* 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_TAURINE_AND_HYPOTAURINE_METABOLISM
KEGG_SELENOAMINO_ACID_METABOLISM
KEGG_GLUTATHIONE_METABOLISM
KEGG_ARACHIDONIC_ACID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GGT1
MedGen: GGT1 (Human Medical Genetics with Condition)
ClinVar: GGT1
PhenotypeMGI: GGT1 (International Mouse Phenotyping Consortium)
PhenomicDB: GGT1

Mutations for GGT1
* 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
pancreasGGT1chr222500851225008532GGT1chr222500893525008955
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 GGT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW182722GGT1288222498160324981689CARS28542913111353839111358446

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample11               
GAIN (# sample)11               
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=11

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=49)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=9)
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
chr22:25023893-25023893p.S428N11
chr22:25011062-25011062p.T117S10
chr22:25010758-25010758p.D60D8
chr22:25023869-25023869p.M421fs*757
chr22:25024072-25024072p.C454F6
chr22:25024076-25024076p.P455P6
chr22:25023903-25023903p.N431N6
chr22:25016296-25016296p.G128G5
chr22:25023915-25023915p.V435V4
chr22:25023492-25023492p.E372K4

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample23141 1 21 2211110825
# mutation22121 1 21 2211110826
nonsynonymous SNV 2 11 1 11 111 15425
synonymous SNV2 11    1  11 1 54 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
chr22:25010828p.G84S,GGT13
chr22:25010758p.D60D,GGT12
chr22:25023893p.S428N,GGT12
chr22:25010819p.T456M,GGT11
chr22:25023938p.A110T,GGT11
chr22:25019114p.A356S,GGT11
chr22:25023478p.T456T,GGT11
chr22:25024063p.V134E,GGT11
chr22:25019156p.I366I,GGT11
chr22:25023483p.T479M,GGT11

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 GGT1 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 GGT1

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

ACSM1,AFMID,AKR1C2,AKR1D1,C15orf43,LRRC75B,CLPSL1,
C6orf223,DBI,GGT1,GGT3P,GGTLC1,GGTLC2,HAAO,
LOC644165,MUCL1,OXER1,SERHL2,SERHL,SPINK8,SULT1C3
ACSL3,ADAM2,AFMID,ALOX15B,B3GAT1,C15orf43,DHCR7,
DHRS2,FIBCD1,GGT1,GGTLC2,HIST1H3D,HMGCS2,MVK,
NSUN2,PNLIPRP3,SERHL2,SERHL,SLC15A1,SPINK8,SRD5A1

ABCB9,ABCC2,ACOT11,AP1B1,BMP7,LRRC75B,CISD3,
COMT,FGFR3,GGT1,GGT3P,GGTLC1,GGTLC2,ID1,
PKLR,PLA2G4F,RAB11FIP4,SCARB1,SMAD6,STX3,ZNRF3
ADIRF,CDH16,CLDN15,CYP3A7,FAM109A,GGT1,GGT3P,
GGTLC1,GGTLC2,HEBP1,KDM8,KCP,NAALADL1,NAT8B,
PKLR,SEC16B,SLC17A8,SLC34A2,TBX3,AGMO,XPNPEP2
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 GGT1
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
DB00143gamma-glutamyltransferase 1approved; nutraceuticalGlutathione


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Cross referenced IDs for GGT1
* 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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