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 B4GALT1
Basic gene info.Gene symbolB4GALT1
Gene nameUDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1
SynonymsB4GAL-T1|CDG2D|GGTB2|GT1|GTB|beta4Gal-T1
CytomapUCSC genome browser: 9p13
Genomic locationchr9 :33110638-33167356
Type of geneprotein-coding
RefGenesNM_001497.3,
Ensembl idENSG00000086062
DescriptionUDP-Gal:beta-GlcNAc beta-1,4-galactosyltransferase 1UDP-galactose:beta-N-acetylglucosamine beta-1,4-galactosyltransferase 1beta-1,4-GalTase 1beta-1,4-galactosyltransferase 1glycoprotein-4-beta-galactosyltransferase 2lactose synthase
Modification date20141219
dbXrefs MIM : 137060
HGNC : HGNC
Ensembl : ENSG00000086062
HPRD : 00659
Vega : OTTHUMG00000019764
ProteinUniProt: P15291
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_B4GALT1
BioGPS: 2683
Gene Expression Atlas: ENSG00000086062
The Human Protein Atlas: ENSG00000086062
PathwayNCI Pathway Interaction Database: B4GALT1
KEGG: B4GALT1
REACTOME: B4GALT1
ConsensusPathDB
Pathway Commons: B4GALT1
MetabolismMetaCyc: B4GALT1
HUMANCyc: B4GALT1
RegulationEnsembl's Regulation: ENSG00000086062
miRBase: chr9 :33,110,638-33,167,356
TargetScan: NM_001497
cisRED: ENSG00000086062
ContextiHOP: B4GALT1
cancer metabolism search in PubMed: B4GALT1
UCL Cancer Institute: B4GALT1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of B4GALT1 in cancer cell metabolism1. Ye Y, Zhou Y, Zhang L, Chen Y, Lyu X, et al. (2013) EBV-miR-BART1 is involved in regulating metabolism-associated genes in nasopharyngeal carcinoma. Biochem Biophys Res Commun 436: 19-24. doi: 10.1016/j.bbrc.2013.05.008. go to article

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Phenotypic Information for B4GALT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: B4GALT1
Familial Cancer Database: B4GALT1
* 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
KEGG_GALACTOSE_METABOLISM
REACTOME_METABOLISM_OF_PROTEINS
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 137060; gene.
137060; gene.
607091; phenotype.
607091; phenotype.
Orphanet 79332; B4GALT1-CDG.
79332; B4GALT1-CDG.
DiseaseKEGG Disease: B4GALT1
MedGen: B4GALT1 (Human Medical Genetics with Condition)
ClinVar: B4GALT1
PhenotypeMGI: B4GALT1 (International Mouse Phenotyping Consortium)
PhenomicDB: B4GALT1

Mutations for B4GALT1
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryB4GALT1chr93311577533115795APTXchr93300085833000878
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows B4GALT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
EC510108NMRAL11521645137404513791B4GALT15313093311122833111316
AI955342B4GALT13621393311064033110817NUDT8214366116739722567397377
BE939488B4GALT12721193311072533110908B4GALT120726693311091833110977
BE466056B4GALT116193311119533111254B4GALT15631093311210633112360

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       2       1
GAIN (# sample)1       2       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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=22)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr9:33113497-33113497p.Y384Y2
chr9:33166973-33166973p.N65N2
chr9:33135276-33135276p.R187W1
chr9:33166879-33166879p.G97C1
chr9:33116073-33116073p.L292P1
chr9:33167151-33167151p.P6R1
chr9:33135281-33135281p.R185H1
chr9:33113458-33113458p.P397P1
chr9:33166892-33166892p.S92S1
chr9:33120442-33120442p.V271I1

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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
# sample13 6       12   24 3
# mutation13 8       12   24 3
nonsynonymous SNV12 7       11   12 2
synonymous SNV 1 1        1   12 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
chr9:33166879p.P183P1
chr9:33120558p.P183L1
chr9:33166892p.P397P1
chr9:33113458p.G164G1
chr9:33120581p.D357E1
chr9:33166913p.V161V1
chr9:33113578p.I341V1
chr9:33120603p.C130F1
chr9:33166952p.R339H1
chr9:33113815p.V119E1

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 B4GALT1 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 B4GALT1

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

B4GALT1,BAG1,CEACAM8,CHST1,CLIC6,ECT2L,ELOVL5,
GHSR,HIGD1A,INSL4,KIAA0087,KSR1,NFX1,P2RX6P,
PLD1,SCGB1D2,SCGB2A2,SLC6A9,SMU1,SPINK4,UBAP1
ARF6,ARRDC3,B4GALT1,CHSY1,FAM60A,GNL3,MFSD6,
NIP7,NOLC1,NOP58,NUFIP1,PPRC1,PVT1,QTRTD1,
RAD18,RBM12,SRSF6,SH3BP4,SLC7A1,TEX10,WDR43

ARFGAP3,B4GALT1,C10orf54,MIR22HG,CCNG2,CD59,CDKN2B,
ELL2,EMP1,EPAS1,GSN,IL4R,KIAA0247,FAM214B,
LHFPL2,PDLIM5,SEC24A,SEC24D,SGMS2,TMEM127,UGCG
ATP2B1,B4GALT1,B4GALT5,DHRS9,DSC2,EHD4,FABP1,
GPD2,HAS3,LANCL3,MAPRE3,MIER3,NT5C2,OXSR1,
RNF6,SLC20A1,STK39,TMEM65,TMPRSS2,XIAP,YWHAB
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 B4GALT1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P15291; -.
ChemistryChEMBL CHEMBL4384; -.
ChemistryBindingDB P15291; -.
ChemistryChEMBL CHEMBL4384; -.
Organism-specific databasesPharmGKB PA25223; -.
Organism-specific databasesPharmGKB PA25223; -.
Organism-specific databasesCTD 2683; -.
Organism-specific databasesCTD 2683; -.

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 1approved; nutraceuticalN-Acetyl-D-glucosamine
DB02696UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1experimental6-Aminohexyl-Uridine-C1,5'-Diphosphate
DB03013UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1experimentalDi(N-Acetyl-D-Glucosamine)
DB03501UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1experimentalUridine Diphosphate Galactose
DB03685UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1experimentalUridine-5'-Monophosphate
DB03814UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1experimental2-(N-Morpholino)-Ethanesulfonic Acid


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Cross referenced IDs for B4GALT1
* 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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