Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 GCNT1
Basic gene info.Gene symbolGCNT1
Gene nameglucosaminyl (N-acetyl) transferase 1, core 2
SynonymsC2GNT|C2GNT-L|C2GNT1|G6NT|NACGT2|NAGCT2
CytomapUCSC genome browser: 9q13
Genomic locationchr9 :79093256-79122332
Type of geneprotein-coding
RefGenesNM_001097633.1,
NM_001097634.1,NM_001097635.1,NM_001097636.1,NM_001490.4,
Ensembl idENSG00000187210
Descriptionbeta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferasebeta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferasebeta-1,6-N-acetylglucosaminyltransferasecore 2 GnTcore 2 beta-1,6-N-acetylglucosam
Modification date20141207
dbXrefs MIM : 600391
HGNC : HGNC
Ensembl : ENSG00000187210
HPRD : 02669
Vega : OTTHUMG00000020044
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GCNT1
BioGPS: 2650
Gene Expression Atlas: ENSG00000187210
The Human Protein Atlas: ENSG00000187210
PathwayNCI Pathway Interaction Database: GCNT1
KEGG: GCNT1
REACTOME: GCNT1
ConsensusPathDB
Pathway Commons: GCNT1
MetabolismMetaCyc: GCNT1
HUMANCyc: GCNT1
RegulationEnsembl's Regulation: ENSG00000187210
miRBase: chr9 :79,093,256-79,122,332
TargetScan: NM_001097633
cisRED: ENSG00000187210
ContextiHOP: GCNT1
cancer metabolism search in PubMed: GCNT1
UCL Cancer Institute: GCNT1
Assigned class in ccmGDBC

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Phenotypic Information for GCNT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GCNT1
Familial Cancer Database: GCNT1
* 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_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GCNT1
MedGen: GCNT1 (Human Medical Genetics with Condition)
ClinVar: GCNT1
PhenotypeMGI: GCNT1 (International Mouse Phenotyping Consortium)
PhenomicDB: GCNT1

Mutations for GCNT1
* 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 GCNT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AJ299263KAT6B1319107678593876786654GCNT130039097904264479043011

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)                 
LOSS (# sample)   1             
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=38)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr9:79117954-79117954p.M219I4
chr9:79118132-79118132p.E279K3
chr9:79118113-79118113p.V272V2
chr9:79117986-79117986p.V230A2
chr9:79118441-79118441p.I382V2
chr9:79117888-79117888p.L197L2
chr9:79118029-79118029p.T244T2
chr9:79117571-79117571p.D92N2
chr9:79118475-79118475p.R393H2
chr9:79117955-79117955p.D220N2

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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
# sample1  101 2 2  103   112 6
# mutation1  101 2 2  104   112 6
nonsynonymous SNV1  81   1  54   71 5
synonymous SNV   2  2 1  5    41 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
chr9:79118029p.T244T,GCNT13
chr9:79118113p.V272V,GCNT12
chr9:79118164p.F289F,GCNT12
chr9:79118407p.P370P,GCNT12
chr9:79117571p.D92N,GCNT12
chr9:79118429p.L22F,GCNT11
chr9:79117652p.A179V,GCNT11
chr9:79117891p.L266L,GCNT11
chr9:79117357p.V23A,GCNT11
chr9:79118080p.S189S,GCNT11

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 GCNT1 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 GCNT1

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

ARHGAP12,BAGE2,C12orf49,CD177,EXOC5,GCNT1,GMFB,
IFNA21,IFNW1,LPGAT1,LRRC16A,OR10J1,IER3___SRGN,PSG11,
PSG2,PSG7,RFK,RMI1,SLC22A10,TEX101,TTLL7
ADAM17,ALDH1A3,ARF6,MB21D2,CHSY1,CRY1,CSNK1A1,
EZR,FZD3,GCNT1,KLK7,LANCL3,MACC1,MFSD6,
MPZL2,PER2,PPP4R1,SFPQ,TES,WEE1,ZNF365

ALAD,ASTE1,CDC14B,CXorf49B,DMRTB1,FAM120A,FBP1,
FKTN,SLC25A3P1,GCNT1,GNAQ,HNRNPK,MYB,RMST,
SH3BGRL2,SLC44A1,SMC5,STRBP,STX17,TBL1XR1,ZNF189
AGGF1,ALDH6A1,TMEM260,CDC14B,COX15,FAM83B,FOXA1,
GATA6,GCNT1,GFOD2,GRB7,HOXB6,HOXB8,IDH1,
KIAA1804,KLF5,LOC80054,NR5A2,NRIP1,SH2D4A,TSKU
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 GCNT1


There's no related Drug.
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Cross referenced IDs for GCNT1
* 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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