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 B3GNT5
Basic gene info.Gene symbolB3GNT5
Gene nameUDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5
SynonymsB3GN-T5|beta3Gn-T5
CytomapUCSC genome browser: 3q28
Genomic locationchr3 :182971031-182991179
Type of geneprotein-coding
RefGenesNM_032047.4,
Ensembl idENSG00000176597
DescriptionBGnT-5UDP-GlcNAc:beta-Gal beta-1,3-N-acetylglucosaminyltransferase 5beta 1,3 N-acetyglucosaminyltransferase Lc3 synthasebeta-1,3-Gn-T5beta-1,3-N-acetylglucosaminyltransferase 5beta-1,3-N-acetylglucosaminyltransferase bGnT-5lactosylceramide 1,3-N-ace
Modification date20141207
dbXrefs MIM : 615333
HGNC : HGNC
Ensembl : ENSG00000176597
HPRD : 12511
Vega : OTTHUMG00000158436
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_B3GNT5
BioGPS: 84002
Gene Expression Atlas: ENSG00000176597
The Human Protein Atlas: ENSG00000176597
PathwayNCI Pathway Interaction Database: B3GNT5
KEGG: B3GNT5
REACTOME: B3GNT5
ConsensusPathDB
Pathway Commons: B3GNT5
MetabolismMetaCyc: B3GNT5
HUMANCyc: B3GNT5
RegulationEnsembl's Regulation: ENSG00000176597
miRBase: chr3 :182,971,031-182,991,179
TargetScan: NM_032047
cisRED: ENSG00000176597
ContextiHOP: B3GNT5
cancer metabolism search in PubMed: B3GNT5
UCL Cancer Institute: B3GNT5
Assigned class in ccmGDBC

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Phenotypic Information for B3GNT5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: B3GNT5
Familial Cancer Database: B3GNT5
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: B3GNT5
MedGen: B3GNT5 (Human Medical Genetics with Condition)
ClinVar: B3GNT5
PhenotypeMGI: B3GNT5 (International Mouse Phenotyping Consortium)
PhenomicDB: B3GNT5

Mutations for B3GNT5
* 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
ovaryB3GNT5chr3182986923182987123B3GNT5chr3182976786182976986
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 B3GNT5 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        2        
GAIN (# sample)        2        
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=29)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr3:182987776-182987776p.L64F2
chr3:182988300-182988300p.Y238*2
chr3:182987919-182987919p.W111C2
chr3:182987774-182987774p.S63F2
chr3:182988433-182988433p.D283N1
chr3:182988032-182988032p.E149G1
chr3:182988250-182988250p.R222C1
chr3:182987814-182987814p.L76F1
chr3:182988441-182988441p.F285F1
chr3:182988034-182988034p.D150H1

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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
# sample2  2  1 1  32   12 5
# mutation6  2  1 1  32   12 6
nonsynonymous SNV6  2    1  3    11 6
synonymous SNV      1     2    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
chr3:182987774p.S63F2
chr3:182987868p.T110T1
chr3:182988259p.F348Y1
chr3:182987890p.L128M1
chr3:182988298p.A375D1
chr3:182987916p.E149G1
chr3:182988310p.Y182C1
chr3:182987968p.P184S1
chr3:182988511p.L189I1
chr3:182988032p.M190I1

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 B3GNT5 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 B3GNT5

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

ANP32E,ATL2,B3GNT5,BCL11A,MSANTD3,COMMD2,DEK,
AMER1,FAM171A1,GMPS,LBR,PPP1CB,RAP2B,SRSF12,
SUV39H2,TTK,TTLL4,UBXN2A,USP1,YEATS2,ZNF462
ABHD13,ATF3,B3GNT5,CCNL1,CHMP1B,DDX3X,DYRK3,
EGR1,FEM1C,IMPA1,KLHL15,LRRC70,MAP3K8,MAPK1IP1L,
MCL1,NCOA7,NR4A2,PPP1R15B,PTGS2,RFXAP,TRIB1

ARL14,B3GNT5,BCL10,BMP2,CASP7,DSC2,HHLA2,
JOSD1,KLF3,KLF4,KRT20,LIMA1,LIPH,LRRC1,
MALL,MXD1,PTPRH,SDCBP2,TIPARP,TMOD3,TNFRSF21
AVPI1,B3GNT5,BCL10,BMP2,C4orf19,DSC2,ABHD17B,
FOSL2,GPATCH1,JOSD1,KLF3,KLF6,MIDN,MIER3,
NET1,PPP1R15B,RBM47,RCAN1,RHPN2,RNF6,SLC35D1
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 B3GNT5


There's no related Drug.
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Cross referenced IDs for B3GNT5
* 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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