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 B4GALT3
Basic gene info.Gene symbolB4GALT3
Gene nameUDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3
Synonymsbeta4Gal-T3
CytomapUCSC genome browser: 1q21-q23
Genomic locationchr1 :161141099-161147758
Type of geneprotein-coding
RefGenesNM_001199873.1,
NM_001199874.1,NM_003779.3,
Ensembl idENSG00000158850
DescriptionUDP-Gal:beta-GlcNAc beta-1,4-galactosyltransferase 3UDP-galactose:beta-N-acetylglucosamine beta-1,4-galactosyltransferase 3b4Gal-T3beta-1,4-GalTase 3beta-1,4-galactosyltransferase 3beta-N-acetylglucosaminyl-glycolipid beta-1,4-galactosyltransferase 3
Modification date20141207
dbXrefs MIM : 604014
HGNC : HGNC
Ensembl : ENSG00000158850
HPRD : 04929
Vega : OTTHUMG00000034348
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_B4GALT3
BioGPS: 8703
Gene Expression Atlas: ENSG00000158850
The Human Protein Atlas: ENSG00000158850
PathwayNCI Pathway Interaction Database: B4GALT3
KEGG: B4GALT3
REACTOME: B4GALT3
ConsensusPathDB
Pathway Commons: B4GALT3
MetabolismMetaCyc: B4GALT3
HUMANCyc: B4GALT3
RegulationEnsembl's Regulation: ENSG00000158850
miRBase: chr1 :161,141,099-161,147,758
TargetScan: NM_001199873
cisRED: ENSG00000158850
ContextiHOP: B4GALT3
cancer metabolism search in PubMed: B4GALT3
UCL Cancer Institute: B4GALT3
Assigned class in ccmGDBC

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Phenotypic Information for B4GALT3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: B4GALT3
Familial Cancer Database: B4GALT3
* 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: B4GALT3
MedGen: B4GALT3 (Human Medical Genetics with Condition)
ClinVar: B4GALT3
PhenotypeMGI: B4GALT3 (International Mouse Phenotyping Consortium)
PhenomicDB: B4GALT3

Mutations for B4GALT3
* 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 B4GALT3 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
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=30)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr1:161143749-161143749p.H194Y2
chr1:161145604-161145604p.L83I2
chr1:161145720-161145720p.P44L2
chr1:161141721-161141721p.R356H2
chr1:161145756-161145756p.R32Q2
chr1:161143511-161143511p.P229P2
chr1:161145843-161145843p.R3Q2
chr1:161141606-161141606p.*394W1
chr1:161144906-161144906p.R122R1
chr1:161141819-161141819p.T323T1

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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
# sample  17      114   25 10
# mutation  17      114   25 12
nonsynonymous SNV  17       14   12 8
synonymous SNV          1     13 4
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
chr1:161141721p.R356H,B4GALT33
chr1:161145604p.L83F,B4GALT32
chr1:161143511p.P229P,B4GALT32
chr1:161141674p.R372C,B4GALT31
chr1:161143404p.R212Q,B4GALT31
chr1:161144895p.M369L,B4GALT31
chr1:161141683p.D195N,B4GALT31
chr1:161143443p.R366H,B4GALT31
chr1:161144906p.H194Y,B4GALT31
chr1:161141691p.F365F,B4GALT31

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 B4GALT3 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 B4GALT3

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

B4GALT3,DEDD,DUSP12,EFNA4,F11R,FLAD1,MSTO1,
NDUFS2,NIT1,PPOX,PRCC,PVRL4,SCAMP3,SDHC,
SSR2,TOMM40L,UBE2Q1,UBQLN4,UFC1,USF1,USP21
APH1A,B4GALT3,SWSAP1,DALRD3,DHRS13,EFNA3,EFNA4,
ELMO3,KIF22,LOC92659,NMRAL1,PGAP2,PPAP2C,PRR19,
PRSS8,RAB25,SAMD10,TMEM125,TMEM198,TRIM28,TSEN54

ADIPOR1,APH1A,B4GALT3,C1orf43,DAP3,DEDD,DUSP12,
FLAD1,HAX1,JTB,LYSMD1,MRPL9,MRPS14,PPOX,
PYCR2,LAMTOR2,SCAMP3,UBE2Q1,UBQLN4,USP21,VPS72
ADCK2,B4GALT3,VWA9,DALRD3,DCAF12,DDX41,DUS1L,
EDEM2,GSS,ICAM3,LIME1,MAPKAPK3,NGLY1,RAB25,
RNASET2,RPIA,SLC35C2,SMAGP,TPST2,TRABD,YDJC
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 B4GALT3
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
DB00141UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3approved; nutraceuticalN-Acetyl-D-glucosamine


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Cross referenced IDs for B4GALT3
* 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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