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 GCNT3
Basic gene info.Gene symbolGCNT3
Gene nameglucosaminyl (N-acetyl) transferase 3, mucin type
SynonymsC2/4GnT|C24GNT|C2GNT2|C2GNTM|GNTM
CytomapUCSC genome browser: 15q21.3
Genomic locationchr15 :59903981-59912210
Type of geneprotein-coding
RefGenesNM_004751.2,
Ensembl idENSG00000140297
DescriptionC2GnT-mucin typebeta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 3beta1,6-N-acetylglucosaminyltransferase-Mbeta1,6GlcNAc-transferasecore 2/core 4 beta-1,6-N-acetylglucosaminyltransferasehC2GnT-Mmucus-type core 2 b
Modification date20141207
dbXrefs MIM : 606836
HGNC : HGNC
Ensembl : ENSG00000140297
HPRD : 06018
Vega : OTTHUMG00000132726
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GCNT3
BioGPS: 9245
Gene Expression Atlas: ENSG00000140297
The Human Protein Atlas: ENSG00000140297
PathwayNCI Pathway Interaction Database: GCNT3
KEGG: GCNT3
REACTOME: GCNT3
ConsensusPathDB
Pathway Commons: GCNT3
MetabolismMetaCyc: GCNT3
HUMANCyc: GCNT3
RegulationEnsembl's Regulation: ENSG00000140297
miRBase: chr15 :59,903,981-59,912,210
TargetScan: NM_004751
cisRED: ENSG00000140297
ContextiHOP: GCNT3
cancer metabolism search in PubMed: GCNT3
UCL Cancer Institute: GCNT3
Assigned class in ccmGDBC

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Phenotypic Information for GCNT3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GCNT3
Familial Cancer Database: GCNT3
* 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: GCNT3
MedGen: GCNT3 (Human Medical Genetics with Condition)
ClinVar: GCNT3
PhenotypeMGI: GCNT3 (International Mouse Phenotyping Consortium)
PhenomicDB: GCNT3

Mutations for GCNT3
* 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 GCNT3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW842590GCNT311360155991092659911275HSP90B135242812104336852104336928

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=32)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr15:59911184-59911184p.R249R3
chr15:59911232-59911232p.W265*2
chr15:59911235-59911235p.K266N2
chr15:59911701-59911701p.Q422*2
chr15:59911741-59911741p.G435V2
chr15:59910953-59910953p.F172F2
chr15:59911535-59911535p.W366*2
chr15:59910672-59910672p.E79Q2
chr15:59911370-59911370p.K311N2
chr15:59910449-59910449p.W4*1

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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
# sample1114  1 1  353  132 4
# mutation2114  1 1  353  132 5
nonsynonymous SNV  14       332  52 3
synonymous SNV21    1 1   21  8  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
chr15:59911184p.R249R3
chr15:59911235p.K266N2
chr15:59911741p.G435E2
chr15:59911513p.F187F1
chr15:59910454p.S359C1
chr15:59910815p.R6K1
chr15:59911580p.D212D1
chr15:59910504p.P381P1
chr15:59910848p.A23T1
chr15:59911283p.F31F1

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 GCNT3 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 GCNT3

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

ATP1B3,ZC2HC1B,CA13,GALR2,GCNT3,GJB6,GPR12,
HYAL4,KCNJ4,KLF5,KRT4,KRT77,LIPI,LOC642929,
MAL,MORC1,PGLYRP3,PRB2,RHCG,SLC9A3,TMEM213
ANXA10,APOH,CTSE,GCNT3,GKN2,HKDC1,IGF2BP1,
KRTAP13-1,MAGEA4,NAPSA,NKX2-1,PAEP,BPIFA1,PSAPL1,
SCGB3A2,SFTA3,SFTPB,SFTPC,SLC26A9,TM4SF5,UGT1A10

ABCG2,B3GALT5,C11orf86,LINC00520,CCDC68,CTSE,DHRS9,
GCNT3,GPR110,HSD17B2,LIPH,MALL,MUC17,PLAC8,
PTPRH,RHOF,SDCBP2,TSPAN1,TSPAN3,VILL,VSIG1
ABHD3,ATP1B3,C5orf30,CAB39,CCDC68,CEACAM1,CEACAM5,
EPS8,ABHD17C,GCNT3,GNA13,MYL12A,PIP4K2C,PIP5K1B,
PLAC8,SLC26A3,SPATS2L,STK24,STX3,TSPAN1,UGP2
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 GCNT3


There's no related Drug.
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Cross referenced IDs for GCNT3
* 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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