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 B3GNT3
Basic gene info.Gene symbolB3GNT3
Gene nameUDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3
SynonymsB3GAL-T8|B3GN-T3|B3GNT-3|HP10328|TMEM3|beta3Gn-T3
CytomapUCSC genome browser: 19p13.1
Genomic locationchr19 :17905918-17924385
Type of geneprotein-coding
RefGenesNM_014256.3,
Ensembl idENSG00000179913
DescriptionUDP-Gal:beta-GlcNAc beta-1,3-galactosyltransferase 8UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase 8beta-1,3-GalTase 8beta-1,3-Gn-T3beta-1,3-N-acetylglucosaminyltransferase bGnT-3beta-3-Gx-T8beta3GalT8core 1 extending beta-1,
Modification date20141207
dbXrefs MIM : 605863
HGNC : HGNC
Ensembl : ENSG00000179913
HPRD : 10431
Vega : OTTHUMG00000183490
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_B3GNT3
BioGPS: 10331
Gene Expression Atlas: ENSG00000179913
The Human Protein Atlas: ENSG00000179913
PathwayNCI Pathway Interaction Database: B3GNT3
KEGG: B3GNT3
REACTOME: B3GNT3
ConsensusPathDB
Pathway Commons: B3GNT3
MetabolismMetaCyc: B3GNT3
HUMANCyc: B3GNT3
RegulationEnsembl's Regulation: ENSG00000179913
miRBase: chr19 :17,905,918-17,924,385
TargetScan: NM_014256
cisRED: ENSG00000179913
ContextiHOP: B3GNT3
cancer metabolism search in PubMed: B3GNT3
UCL Cancer Institute: B3GNT3
Assigned class in ccmGDBC

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Phenotypic Information for B3GNT3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: B3GNT3
Familial Cancer Database: B3GNT3
* 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
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: B3GNT3
MedGen: B3GNT3 (Human Medical Genetics with Condition)
ClinVar: B3GNT3
PhenotypeMGI: B3GNT3 (International Mouse Phenotyping Consortium)
PhenomicDB: B3GNT3

Mutations for B3GNT3
* 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 B3GNT3 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=34)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr19:17919127-17919127p.G171R3
chr19:17922515-17922515p.V235M3
chr19:17918748-17918748p.P44P3
chr19:17919016-17919016p.R134S2
chr19:17922795-17922795p.R328H2
chr19:17919024-17919024p.V136V2
chr19:17918809-17918809p.T65A2
chr19:17922427-17922427p.F205F2
chr19:17918850-17918850p.Q78H2
chr19:17922535-17922535p.N241N1

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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
# sample12143 3 1  15  1127 5
# mutation12143 3 1  15  1147 5
nonsynonymous SNV11122 3 1  14  166 5
synonymous SNV 1 21       1   81  
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
chr19:17918980p.R122C2
chr19:17922427p.G171R2
chr19:17919127p.F205F2
chr19:17922600p.I245T1
chr19:17922734p.Y337Y1
chr19:17918894p.E256Q1
chr19:17922419p.R338Q1
chr19:17922646p.R122H1
chr19:17922801p.V258V1
chr19:17918965p.R345C1

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 B3GNT3 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 B3GNT3

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

ACTR3,AQP5,B3GNT3,B3GNT7,BACE2,LINC01559,CDH3,
FAM3D,GPR110,KCNN4,MALL,MPZL2,NCOA7,PADI2,
PERP,RASAL1,RNF145,SLC35C1,STX19,UGP2,UGT2B7
ASIC1,B3GNT3,C10orf90,MYRF,CHRM1,CRABP1,DTNB,
ELF5,EPHB3,FAM81A,FOLH1,KCNN4,NEURL3,PLCH1,
RASAL1,RASGEF1C,ROPN1,SLC13A2,SOX8,TGFA,UGT8

ACOX1,B3GNT3,CACFD1,CDH1,CDHR5,CEACAM1,CEACAM5,
CLDN23,KIAA1161,LOC100130933,MANSC1,MEP1A,MYO15B,NR2F6,
PGPEP1,PRSS8,SLC35D1,SMPD1,ST14,STAP2,TMBIM1
B3GNT3,BAIAP2L1,C4orf19,CLDN4,CRB3,DNM2,ELF4,
F2RL1,IRF6,KRT18,KRT8,LIPH,LSR,LYPLA2,
MARK2,PCSK7,PKP3,SH3RF1,SLC35D1,SPATA2,ZDHHC5
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 B3GNT3


There's no related Drug.
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Cross referenced IDs for B3GNT3
* 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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