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 GNGT1
Basic gene info.Gene symbolGNGT1
Gene nameguanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1
SynonymsGNG1
CytomapUCSC genome browser: 7q21.3
Genomic locationchr7 :93535819-93540485
Type of geneprotein-coding
RefGenesNM_021955.3,
Ensembl idENSG00000127928
Descriptionguanine nucleotide-binding protein G(T) subunit gamma-T1transducin gamma chain
Modification date20141207
dbXrefs MIM : 189970
HGNC : HGNC
Ensembl : ENSG00000127928
HPRD : 01805
Vega : OTTHUMG00000022908
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNGT1
BioGPS: 2792
Gene Expression Atlas: ENSG00000127928
The Human Protein Atlas: ENSG00000127928
PathwayNCI Pathway Interaction Database: GNGT1
KEGG: GNGT1
REACTOME: GNGT1
ConsensusPathDB
Pathway Commons: GNGT1
MetabolismMetaCyc: GNGT1
HUMANCyc: GNGT1
RegulationEnsembl's Regulation: ENSG00000127928
miRBase: chr7 :93,535,819-93,540,485
TargetScan: NM_021955
cisRED: ENSG00000127928
ContextiHOP: GNGT1
cancer metabolism search in PubMed: GNGT1
UCL Cancer Institute: GNGT1
Assigned class in ccmGDBC

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Phenotypic Information for GNGT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GNGT1
Familial Cancer Database: GNGT1
* 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
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GNGT1
MedGen: GNGT1 (Human Medical Genetics with Condition)
ClinVar: GNGT1
PhenotypeMGI: GNGT1 (International Mouse Phenotyping Consortium)
PhenomicDB: GNGT1

Mutations for GNGT1
* 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 GNGT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF986197GNGT11720479351605493516607GLG1199405167451422474519729
X93851PSD318081844128718441366GNGT17623079334682493346977
AA303013TMCO3122613114204317114204542GNGT122328179351606893516126
BI050757PPP1R21114524872582548734469GNGT114119879351847893518535
BM983864PARD3B2212205874391205874410GNGT11839879351585993516603
AW995893GNGT13028979351667393518535UBE2I2724371613750241375189

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=8)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr7:93536070-93536070p.I4I1
chr7:93540158-93540158p.D51E1
chr7:93536082-93536082p.D8E1
chr7:93540172-93540172p.G56D1
chr7:93536106-93536106p.K16K1
chr7:93540176-93540176p.I57I1
chr7:93536107-93536107p.M17L1
chr7:93540182-93540182p.E59E1
chr7:93536131-93536131p.E25*1
chr7:93540200-93540200p.K65K1

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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
# sample   1       31 1 1111
# mutation   1       31 1 1111
nonsynonymous SNV   1       3  1  11 
synonymous SNV            1   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
chr7:93536082p.M31K1
chr7:93536150p.V40I1
chr7:93540123p.G56D1
chr7:93540172p.E59E1
chr7:93540182p.K65K1
chr7:93540200p.E66Q1
chr7:93540201p.E66D1
chr7:93540203p.V3L1
chr7:93536065p.I4I1
chr7:93536070p.D8E1

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 GNGT1 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 GNGT1

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

ADAMTS20,ALG1L,C12orf56,COA1,DEFB126,COL6A4P1,SPATA31D3,
GJB7,GNGT1,GRK7,H2BFWT,HTR2C,KRTAP4-1,MCHR2,
OR13H1,OR8D2,SLC25A2,SLC5A12,SPDYC,SPERT,TAS2R38
LINC01559,C7orf72,FAM151A,GNGT1,HNF1B,CEMIP,KRTAP4-1,
LGSN,MAGEA4,NAPSA,NMU,OR13H1,OTOP2,SCEL,
SCGB3A2,SERPINB3,SFTPB,TDRG1,TM4SF20,TR

C1orf111,RBM48,CALCR,CARD18,CGB2,GNGT1,INSM2,
KRTAP27-1,LOC493754,LRCH4,NBPF6,PCLO,POLR2J4,RFPL2,
RIMS2,RTP2,SBDSP1,SIM1,SLC12A9,TAS2R7,UNC5A
ABCG2,AMDHD2,KIAA1551,SH3D21,CACNA1D,COX6A2,CXADRP3,
GLS,GNGT1,JMJD1C,KRT13,LOC154449,MGC27382,MIA2,
OSGIN1,RSPH3,SLC16A5,SLC22A18,SLC26A1,TYW1B,UGT1A1
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 GNGT1
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
DB07752guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1experimentalFARNESYL
DB00945guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedAcetylsalicylic acid
DB00394guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedBeclomethasone
DB00443guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedBetamethasone
DB01222guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approved; investigationalBudesonide
DB01410guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approved; investigationalCiclesonide
DB01260guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approved; investigationalDesonide
DB01234guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approved; investigationalDexamethasone
DB00180guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approved; investigationalFlunisolide
DB00588guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approved; investigationalFluticasone Propionate
DB00741guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedHydrocortisone
DB00959guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedMethylprednisolone
DB00764guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedMometasone
DB01384guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedParamethasone
DB00860guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedPrednisolone
DB00635guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedPrednisone
DB00896guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedRimexolone
DB00620guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedTriamcinolone
DB00125guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approved; nutraceuticalL-Arginine
DB00155guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approved; nutraceuticalL-Citrulline
DB00435guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedNitric Oxide
DB00988guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedDopamine
DB00171guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approved; nutraceuticalAdenosine triphosphate
DB00131guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approved; nutraceuticalAdenosine monophosphate
DB00396guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1approvedProgesterone


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Cross referenced IDs for GNGT1
* 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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