Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 B3GAT2
Basic gene info.Gene symbolB3GAT2
Gene namebeta-1,3-glucuronyltransferase 2
SynonymsGLCATS
CytomapUCSC genome browser: 6q13
Genomic locationchr6 :71571068-71666788
Type of geneprotein-coding
RefGenesNM_080742.2,
Ensembl idENSG00000112309
DescriptionUDP-glucuronosyltransferase SUDP-glucuronyltransferase Sgalactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2glcAT-Dglucuronosyltransferase Suridine diphosphate glucuronic acid:acceptor glucuronosyltransferase
Modification date20141207
dbXrefs MIM : 607497
HGNC : HGNC
HPRD : 06325
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_B3GAT2
BioGPS: 135152
Gene Expression Atlas: ENSG00000112309
The Human Protein Atlas: ENSG00000112309
PathwayNCI Pathway Interaction Database: B3GAT2
KEGG: B3GAT2
REACTOME: B3GAT2
ConsensusPathDB
Pathway Commons: B3GAT2
MetabolismMetaCyc: B3GAT2
HUMANCyc: B3GAT2
RegulationEnsembl's Regulation: ENSG00000112309
miRBase: chr6 :71,571,068-71,666,788
TargetScan: NM_080742
cisRED: ENSG00000112309
ContextiHOP: B3GAT2
cancer metabolism search in PubMed: B3GAT2
UCL Cancer Institute: B3GAT2
Assigned class in ccmGDBC

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Phenotypic Information for B3GAT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: B3GAT2
Familial Cancer Database: B3GAT2
* 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_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: B3GAT2
MedGen: B3GAT2 (Human Medical Genetics with Condition)
ClinVar: B3GAT2
PhenotypeMGI: B3GAT2 (International Mouse Phenotyping Consortium)
PhenomicDB: B3GAT2

Mutations for B3GAT2
* 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
skinB3GAT2chr67159367171593671chr67240320072403200
skinB3GAT2chr67159837871598378chr67905053479050534
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 B3GAT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DR002957B3GAT2323267166601971666248SMAP122655367157154471665584

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 # sample2         1      
GAIN (# sample)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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=17)
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
chr6:71665986-71665986p.G49G7
chr6:71603924-71603924p.R215R3
chr6:71603921-71603921p.R216C2
chr6:71603926-71603926p.G214V1
chr6:71571408-71571408p.N310K1
chr6:71665781-71665781p.D118Y1
chr6:71571627-71571627p.R264H1
chr6:71603934-71603934p.L211L1
chr6:71571416-71571416p.L308I1
chr6:71665793-71665793p.I114V1

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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
# sample31 4    2  622  26 4
# mutation31 5    2  622  26 4
nonsynonymous SNV21 1    1  421  23 1
synonymous SNV1  4    1  2 1   3 3
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
chr6:71665793p.L308I1
chr6:71571416p.G214V1
chr6:71603871p.V306I1
chr6:71665845p.L211L1
chr6:71571422p.L297L1
chr6:71603883p.R199G1
chr6:71665860p.T294N1
chr6:71571447p.L167L1
chr6:71603888p.P288P1
chr6:71665875p.D118Y1

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 B3GAT2 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 B3GAT2

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

B3GAT2,B4GALT6,BCL11A,BCL2L14,CDKAL1,CEP170,DKFZP434L187,
DPYSL5,E2F3,ETV6,PAXBP1,LRP6,NLRP7,OSTN,
PRTFDC1,RNF138,TET1,TMEFF1,TMEM151B,TNFSF15,ZNF507
CARF,ATXN7L1,B3GAT2,TYW5,FLJ10213,KANSL1,LOC283922,
LRIG2,NAA16,NPHP3,PGAP1,PPP1R12A,RNF169,SETD2,
SNORD116-28,UHRF2,XIST,ZNF197,ZNF354B,ZNF431,ZSCAN23

AGAP4,AGAP6,AHSA2,B3GAT2,CCNL2,CHKB-CPT1B,CSAD,
INE1,LENG8,LOC100128842,LOC90834,LOC91316,LY6G5B,MALAT1,
NKTR,PNISR,TAS2R14,WASH7P,WDR27,CFAP44,ZNF767P
B3GAT2,N4BP2L2-IT2,FAM13A-AS1,FDPSP2,FLJ10213,LINC01000,INE1,
LOC100190986,LOC90834,LY6G5B,MALAT1,MDM4,HNRNPU-AS1,NFAT5,
NKTR,PCGF3,RPL23AP64,TRIM33,UBN2,ZBTB43,ZNF789
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 B3GAT2


There's no related Drug.
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Cross referenced IDs for B3GAT2
* 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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