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 B3GNT2
Basic gene info.Gene symbolB3GNT2
Gene nameUDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2
SynonymsB3GN-T2|B3GNT|B3GNT-2|B3GNT1|BETA3GNT|BGNT2|BGnT-2
CytomapUCSC genome browser: 2p15
Genomic locationchr2 :62423261-62451866
Type of geneprotein-coding
RefGenesNM_006577.5,
NM_033252.1,
Ensembl idENSG00000170340
DescriptionUDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1beta-1,3-Gn-T1beta-1,3-Gn-T2beta-1,3-N-acetylglucosaminyltransferase bGnT-1beta-1,3-N-acetylglucosaminyltransferase bGnT-2beta3Gn-T1beta3Gn-T2
Modification date20141207
dbXrefs MIM : 605581
HGNC : HGNC
Ensembl : ENSG00000170340
HPRD : 09279
Vega : OTTHUMG00000129444
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_B3GNT2
BioGPS: 10678
Gene Expression Atlas: ENSG00000170340
The Human Protein Atlas: ENSG00000170340
PathwayNCI Pathway Interaction Database: B3GNT2
KEGG: B3GNT2
REACTOME: B3GNT2
ConsensusPathDB
Pathway Commons: B3GNT2
MetabolismMetaCyc: B3GNT2
HUMANCyc: B3GNT2
RegulationEnsembl's Regulation: ENSG00000170340
miRBase: chr2 :62,423,261-62,451,866
TargetScan: NM_006577
cisRED: ENSG00000170340
ContextiHOP: B3GNT2
cancer metabolism search in PubMed: B3GNT2
UCL Cancer Institute: B3GNT2
Assigned class in ccmGDBC

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Phenotypic Information for B3GNT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: B3GNT2
Familial Cancer Database: B3GNT2
* 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: B3GNT2
MedGen: B3GNT2 (Human Medical Genetics with Condition)
ClinVar: B3GNT2
PhenotypeMGI: B3GNT2 (International Mouse Phenotyping Consortium)
PhenomicDB: B3GNT2

Mutations for B3GNT2
* 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
pancreasB3GNT2chr26244705362447073NRXN1chr25036012550360145
pancreasB3GNT2chr26244845462448474NRXN1chr25087971550879735
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 B3GNT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AF288209MALAT1166116527309865273163B3GNT262249826244938762451866
AV724042CNTN41120330788933079012B3GNT211769326244961362450198

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=26)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=2)
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
chr2:62449733-62449733p.R126R2
chr2:62449779-62449779p.P142S2
chr2:62449968-62449968p.H205Y2
chr2:62449632-62449632p.L93L2
chr2:62450208-62450208p.K285E2
chr2:62450265-62450265p.A304T1
chr2:62449434-62449434p.V27I1
chr2:62449892-62449892p.V179V1
chr2:62450292-62450292p.G313S1
chr2:62449456-62449456p.N36fs*61

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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
# sample21 51 1 2  421  42 3
# mutation21 61 1 2  721  42 3
nonsynonymous SNV11 41 1 2  311  22 1
synonymous SNV1  2       41   2  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
chr2:62449632p.L93L2
chr2:62449598p.K285E1
chr2:62449880p.S297S1
chr2:62450306p.C96C1
chr2:62449607p.R126H1
chr2:62449892p.G313S1
chr2:62450312p.R126R1
chr2:62449618p.L317L1
chr2:62449926p.D136H1
chr2:62450343p.L319L1

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 B3GNT2 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 B3GNT2

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

AAK1,ACTR2,AFTPH,B3GNT2,C2orf69,FBXO11,KIAA1033,
LOC284441,MCFD2,MOB1A,PAPOLG,PEX13,PPM1B,PPP3R1,
RAB1A,RTN4,SLC30A6,SMEK2,SP3,UBXN4,USP34
AEBP2,ARF6,B3GNT2,C5orf28,DENND6A,FAM60A,IRF2BP2,
MED17,MEX3C,NUP35,PACRGL,PIGA,PRKCI,RBM12,
RYBP,SRSF6,SOX9,TMEM161B,TWISTNB,YTHDF2,ZDHHC13

ARPC2,B3GNT2,B3GNT5,BZW1,CD59,COQ10B,DNAJB9,
ERO1L,ERRFI1,GNA13,IFNGR1,PELI1,PLAUR,PLIN3,
PPP3R1,RAP1B,REEP3,SLC20A1,TGFA,TMBIM1,UGCG
AMACR,ATP1B3,B3GNT2,C12orf75,CYB5B,DHX32,EPS8,
FKBP1A,LNX2,LOC100130933,MINPP1,NCEH1,NUDT4,PIP5K1B,
RNF138,SLC17A5,STYK1,TMCO1,TSPAN1,TSPAN3,VAPA
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 B3GNT2


There's no related Drug.
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Cross referenced IDs for B3GNT2
* 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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