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 GGT5
Basic gene info.Gene symbolGGT5
Gene namegamma-glutamyltransferase 5
SynonymsGGL|GGT 5|GGT-REL|GGTLA1
CytomapUCSC genome browser: 22q11.23
Genomic locationchr22 :24615621-24641110
Type of geneprotein-coding
RefGenesNM_001099781.2,
NM_001099782.2,NM_001302464.1,NM_001302465.1,NM_004121.3,
Ensembl idENSG00000099998
Descriptiongamma-glutamyl cleaving enzymegamma-glutamyl transpeptidase-related enzymegamma-glutamyl transpeptidase-related proteingamma-glutamyltransferase-like activity 1gamma-glutamyltranspeptidase 5glutathione hydrolase 5leukotriene-C4 hydrolase
Modification date20141215
dbXrefs MIM : 137168
HGNC : HGNC
Ensembl : ENSG00000099998
HPRD : 00666
Vega : OTTHUMG00000150796
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GGT5
BioGPS: 2687
Gene Expression Atlas: ENSG00000099998
The Human Protein Atlas: ENSG00000099998
PathwayNCI Pathway Interaction Database: GGT5
KEGG: GGT5
REACTOME: GGT5
ConsensusPathDB
Pathway Commons: GGT5
MetabolismMetaCyc: GGT5
HUMANCyc: GGT5
RegulationEnsembl's Regulation: ENSG00000099998
miRBase: chr22 :24,615,621-24,641,110
TargetScan: NM_001099781
cisRED: ENSG00000099998
ContextiHOP: GGT5
cancer metabolism search in PubMed: GGT5
UCL Cancer Institute: GGT5
Assigned class in ccmGDBC

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Phenotypic Information for GGT5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GGT5
Familial Cancer Database: GGT5
* 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: GGT5
MedGen: GGT5 (Human Medical Genetics with Condition)
ClinVar: GGT5
PhenotypeMGI: GGT5 (International Mouse Phenotyping Consortium)
PhenomicDB: GGT5

Mutations for GGT5
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GGT5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample1                
GAIN (# sample)1                
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=4

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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=20)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

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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
chr22:24621549-24621549p.R434Q4
chr22:24628803-24628803p.A195V3
chr22:24622608-24622608p.P343P3
chr22:24620978-24620978p.P534T2
chr22:24621319-24621319p.R466H2
chr22:24640618-24640618p.A26T2
chr22:24628845-24628845p.S181I2
chr22:24622188-24622188p.R362H2
chr22:24622189-24622189p.R362C2
chr22:24615946-24615946p.G585S2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   141 3 2  232 2103 5
# mutation   121 3 2  242 283 5
nonsynonymous SNV   101 2 2  222 14  3
synonymous SNV   2  1     2  143 2
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
chr22:24621549p.R402Q,GGT54
chr22:24628803p.A163V,GGT53
chr22:24615946p.T293T,GGT52
chr22:24622608p.G553S,GGT52
chr22:24622662p.P311P,GGT52
chr22:24621000p.S451L,GGT51
chr22:24640602p.G305G,GGT51
chr22:24622120p.R434H,GGT51
chr22:24622670p.S407S,GGT51
chr22:24621019p.V291I,GGT51

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 GGT5 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 GGT5

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

ACVRL1,CLDN5,COL18A1,CYGB,EFEMP2,ENG,GGT5,
GRASP,HIC1,HSPA12B,IFFO1,KANK3,LTC4S,LYL1,
MFRP,NAALADL1,NNMT,PTGIR,TGFB1,TMEM204,USHBP1
AIP,ARHGDIA,ARPC1B,EFHD2,GGT5,GIMAP1,HAUS7,
HDAC7,KCTD17,LYL1,MAP3K11,MVP,PLOD3,PPP1R12C,
RNH1,RPS6KA4,SHKBP1,SIPA1,SLC39A13,TNIP2,ZNF668

BGN,VSTM4,C1R,C1S,COL6A2,EFEMP2,EVC2,
FBLN2,GGT5,LHFP,MRAS,MSC,MXRA8,OLFML1,
OLFML2B,PDGFRB,PNMAL2,PRICKLE1,SERPINF1,SERPING1,VIM
ADAM22,ALOX5,BARX1,BMPER,BMX,CCDC129,ENG,
GANAB,GGT5,IL1R1,LRRC32,MKL2,OVCH1,PLVAP,
PTK7,S1PR2,SCARA5,TAS1R3,TBX2,UTRN,ZNF732
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 GGT5
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 5approved; nutraceuticalGlutathione
DB00145gamma-glutamyltransferase 5approved; nutraceuticalGlycine


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Cross referenced IDs for GGT5
* 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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