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 B4GALT2
Basic gene info.Gene symbolB4GALT2
Gene nameUDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 2
SynonymsB4Gal-T2|B4Gal-T3|beta4Gal-T2
CytomapUCSC genome browser: 1p34-p33
Genomic locationchr1 :44445607-44456843
Type of geneprotein-coding
RefGenesNM_001005417.2,
NM_003780.4,NM_030587.2,
Ensembl idENSG00000117411
DescriptionUDP-Gal:beta-GlcNAc beta-1,4-galactosyltransferase 2UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase 2UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 2UDP-galactose:beta-N-acetylglucosamine beta-1,4-galactosyltransferase 2beta-1,4-Gal
Modification date20141207
dbXrefs MIM : 604013
HGNC : HGNC
Ensembl : ENSG00000117411
HPRD : 04928
Vega : OTTHUMG00000008296
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_B4GALT2
BioGPS: 8704
Gene Expression Atlas: ENSG00000117411
The Human Protein Atlas: ENSG00000117411
PathwayNCI Pathway Interaction Database: B4GALT2
KEGG: B4GALT2
REACTOME: B4GALT2
ConsensusPathDB
Pathway Commons: B4GALT2
MetabolismMetaCyc: B4GALT2
HUMANCyc: B4GALT2
RegulationEnsembl's Regulation: ENSG00000117411
miRBase: chr1 :44,445,607-44,456,843
TargetScan: NM_001005417
cisRED: ENSG00000117411
ContextiHOP: B4GALT2
cancer metabolism search in PubMed: B4GALT2
UCL Cancer Institute: B4GALT2
Assigned class in ccmGDBC

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Phenotypic Information for B4GALT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: B4GALT2
Familial Cancer Database: B4GALT2
* 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
Orphanet
DiseaseKEGG Disease: B4GALT2
MedGen: B4GALT2 (Human Medical Genetics with Condition)
ClinVar: B4GALT2
PhenotypeMGI: B4GALT2 (International Mouse Phenotyping Consortium)
PhenomicDB: B4GALT2

Mutations for B4GALT2
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryB4GALT2chr14444950444449524IPO13chr14441488744414907
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 B4GALT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CA337099B4GALT2142514445126344456362B4GALT241459214445665944456837
M78136MACF16315313971061839710708B4GALT215332914444703844447428

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   1      
GAIN (# sample)          1      
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=27)
Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr1:44451234-44451234p.I303I3
chr1:44447558-44447558p.R171W2
chr1:44450559-44450559p.R191Q2
chr1:44450969-44450969p.F254L2
chr1:44450592-44450592p.A202V2
chr1:44455983-44455983p.Q328K2
chr1:44447485-44447485p.A146A2
chr1:44456091-44456091p.R364W2
chr1:44446880-44446880p.V16V1
chr1:44451230-44451230p.R302Q1

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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  71 3    421 147 7
# mutation1  61 3    421 146 7
nonsynonymous SNV   51 3    4 1 115 5
synonymous SNV1  1  1     2   31 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
chr1:44456091p.R364W,B4GALT23
chr1:44456112p.R371W,B4GALT22
chr1:44447558p.F254L,B4GALT22
chr1:44450969p.R171W,B4GALT22
chr1:44446880p.V16V,B4GALT21
chr1:44456098p.D216N,B4GALT21
chr1:44450559p.P366L,B4GALT21
chr1:44450970p.A27T,B4GALT21
chr1:44446911p.D223Y,B4GALT21
chr1:44456099p.P366P,B4GALT21

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 B4GALT2 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 B4GALT2

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

ADPRHL2,ATAD3A,B4GALT2,CDC20,CTU2,DAZAP1,DPH2,
EBNA1BP2,ERI3,MAGOH,MED8,MUTYH,NDUFS5,POLR2F,
PPIH,PPP1R14B,RNF220,RRP1,UQCRH,UQCRHL,YBX1
ANXA11,AP2M1,B4GALT2,KXD1,C1orf216,CCM2,DCTN2,
EFEMP2,ISOC2,ITFG3,NAA38,MON1A,PSMB5,PSMB6,
PSMC3,SEC13,STOML1,TXNL4A,UROD,USF2,YIF1A

ADPRHL2,B4GALT2,BTBD6,C14orf80,RBFA,C1orf122,ERI3,
GNL2,HRAS,NOC2L,NUDT8,PEF1,POLR2L,PUSL1,
RNF220,SAC3D1,TMEM125,TMEM134,TMEM39B,TMEM52,TXNL4A
B4GALT2,CALU,CLUAP1,CUEDC1,DEGS1,KDELC1,KLHL23,
LPPR2,LRRC20,LZTS2,MAGED2,NRSN2,NT5M,PEA15,
PTMS,RPL23AP82,SLC39A13,SRPK3,ST3GAL3,TEAD2,TNFSF12
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 B4GALT2
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 2approved; nutraceuticalN-Acetyl-D-glucosamine


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Cross referenced IDs for B4GALT2
* 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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