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 GGT7
Basic gene info.Gene symbolGGT7
Gene namegamma-glutamyltransferase 7
SynonymsD20S101|GGT4|GGTL3|GGTL5|dJ18C9.2
CytomapUCSC genome browser: 20q11.22
Genomic locationchr20 :33432522-33460661
Type of geneprotein-coding
RefGenesNM_178026.2,
Ensembl idENSG00000131067
DescriptionGGT 7gamma-glutamyltransferase 4gamma-glutamyltransferase-like 3gamma-glutamyltransferase-like 5gamma-glutamyltranspeptidase 7gamma-glutamyltranspeptidase-like 3glutathione hydrolase 7
Modification date20141207
dbXrefs MIM : 612342
HGNC : HGNC
Ensembl : ENSG00000131067
HPRD : 07488
Vega : OTTHUMG00000032314
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GGT7
BioGPS: 2686
Gene Expression Atlas: ENSG00000131067
The Human Protein Atlas: ENSG00000131067
PathwayNCI Pathway Interaction Database: GGT7
KEGG: GGT7
REACTOME: GGT7
ConsensusPathDB
Pathway Commons: GGT7
MetabolismMetaCyc: GGT7
HUMANCyc: GGT7
RegulationEnsembl's Regulation: ENSG00000131067
miRBase: chr20 :33,432,522-33,460,661
TargetScan: NM_178026
cisRED: ENSG00000131067
ContextiHOP: GGT7
cancer metabolism search in PubMed: GGT7
UCL Cancer Institute: GGT7
Assigned class in ccmGDBC

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Phenotypic Information for GGT7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GGT7
Familial Cancer Database: GGT7
* 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: GGT7
MedGen: GGT7 (Human Medical Genetics with Condition)
ClinVar: GGT7
PhenotypeMGI: GGT7 (International Mouse Phenotyping Consortium)
PhenomicDB: GGT7

Mutations for GGT7
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
ovaryGGT7chr203345610233456122ZNF341chr203237185932371879
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 GGT7 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
H19810GGT71182203343315233437803CREBBP1834411637769783777235
BI043619GGT727285203344405333444310PIGC2783941172411581172411697
BE501149GGT71376203343296733437811SPEG3724842220344398220344510

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 # sample      1          
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=25)
Stat. for Synonymous SNVs
(# total SNVs=13)
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
chr20:33451148-33451148p.L125L3
chr20:33433205-33433205p.R639*2
chr20:33437795-33437795p.P598P2
chr20:33449360-33449360p.G188V2
chr20:33451191-33451191p.I110I2
chr20:33449261-33449261p.S221F2
chr20:33450711-33450711p.E155*2
chr20:33447366-33447366p.P298P1
chr20:33440034-33440034p.S504L1
chr20:33449295-33449295p.P210S1

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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
# sample2  6  3 4  332  95 3
# mutation3  6  3 4  332  115 4
nonsynonymous SNV3  4    3  32   64 2
synonymous SNV   2  3 1   12  51 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
chr20:33437795p.I110I2
chr20:33444618p.V365M2
chr20:33451191p.S221F2
chr20:33449261p.P598P2
chr20:33449298p.H597Q1
chr20:33440073p.P425P1
chr20:33437798p.R197Q1
chr20:33449333p.D589N1
chr20:33440233p.A404V1
chr20:33444642p.D194V1

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 GGT7 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 GGT7

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

CEP250,DYNLRB1,EDEM2,EEF1A2,EIF6,ERGIC3,GGT7,
GSS,MAP1LC3A,MMP24,MYH7B,NEURL4,NPEPL1,PIGU,
RBMY1E,ROMO1,SCAND1,SSTR1,TRPC4AP,U
CADM4,CNTROB,DDR1,DGCR2,DNAL4,DVL2,ELMO3,
EPS8L2,FBXO44,FZR1,GGT7,PHLDB3,PRKCZ,SFI1,
SGSM2,SH2D3A,SH3GLB2,SLC4A3,SSH3,SYTL1,ZNF324

ASXL1,ATP9A,AAR2,RTFDC1,CHMP4B,DDX27,DIDO1,
ERGIC3,GGT7,GPR56,LOC647979,NCOA6,PCIF1,PCMTD2,
POFUT1,PRPF6,RNF43,SNHG11,TM9SF4,TRPC4AP,ZSWIM3
ARHGAP36,ATP2C2,ERICH5,CLDN8,CPA6,FRZB,GGT7,
GP2,HEPACAM2,HPCA,IL1R2,KIAA1324,LOC100130872,NRAP,
RIMS4,RXFP4,SCGB2A1,STARD10,TMEM38A,WNK4,ZNF774
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 GGT7


There's no related Drug.
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Cross referenced IDs for GGT7
* 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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