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 B4GALT5
Basic gene info.Gene symbolB4GALT5
Gene nameUDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5
SynonymsB4Gal-T5|BETA4-GALT-IV|beta4Gal-T5|beta4GalT-V|gt-V
CytomapUCSC genome browser: 20q13.1-q13.2
Genomic locationchr20 :48249482-48330421
Type of geneprotein-coding
RefGenesNM_004776.3,
Ensembl idENSG00000158470
DescriptionUDP-Gal:beta-GlcNAc beta-1,4-galactosyltransferase 5UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5UDP-galactose:beta-N-acetylglucosamine beta-1,4-galactosyltransferase 5beta-1,4-GalT IIbeta-1,4-GalT IVbeta-1,4-GalTase 5beta-1,4-gal
Modification date20141207
dbXrefs MIM : 604016
HGNC : HGNC
Ensembl : ENSG00000158470
HPRD : 06807
Vega : OTTHUMG00000033086
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_B4GALT5
BioGPS: 9334
Gene Expression Atlas: ENSG00000158470
The Human Protein Atlas: ENSG00000158470
PathwayNCI Pathway Interaction Database: B4GALT5
KEGG: B4GALT5
REACTOME: B4GALT5
ConsensusPathDB
Pathway Commons: B4GALT5
MetabolismMetaCyc: B4GALT5
HUMANCyc: B4GALT5
RegulationEnsembl's Regulation: ENSG00000158470
miRBase: chr20 :48,249,482-48,330,421
TargetScan: NM_004776
cisRED: ENSG00000158470
ContextiHOP: B4GALT5
cancer metabolism search in PubMed: B4GALT5
UCL Cancer Institute: B4GALT5
Assigned class in ccmGDBC

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Phenotypic Information for B4GALT5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: B4GALT5
Familial Cancer Database: B4GALT5
* 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: B4GALT5
MedGen: B4GALT5 (Human Medical Genetics with Condition)
ClinVar: B4GALT5
PhenotypeMGI: B4GALT5 (International Mouse Phenotyping Consortium)
PhenomicDB: B4GALT5

Mutations for B4GALT5
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows B4GALT5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG766572NIPAL3137112479741824797788B4GALT5366822204825069348251153
DB237731SLC12A61227153461076234610988B4GALT5225565204826009948273242
BF812681B4GALT58207204825262148252821PTK719930364311304543113150
BU955750B4GALT53387204825253448252918HSP90AA138266614102549382102549908
CN280929SNX212075122110818122131078B4GALT5204468204824949248249756
CX164716B4GALT51177204825083548251011CKB17857414103987747103988721
AW376281B4GALT56390204825255348252939HNRNPA1382619125467636154676937
AA902204TAF5L13281229728915229729242B4GALT5326584204825284448253983
AI207637DHCR24153315531650355317035B4GALT5518631204825218348252296
BF851864B4GALT52219204827691848277135FBXW421237310103432775103433376

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 # sample6  1  1 1     1  
GAIN (# sample)6  1  1 1     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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=32)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr20:48257081-48257081p.R243H3
chr20:48330222-48330222p.R2R2
chr20:48256282-48256282p.R284W2
chr20:48259034-48259034p.L193L2
chr20:48253947-48253947p.P317L2
chr20:48273211-48273211p.A48A2
chr20:48263586-48263586p.T94S1
chr20:48256242-48256242p.G297D1
chr20:48257133-48257133p.D226Y1
chr20:48260100-48260100p.G151D1

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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
# sample 2 6  2 2  432  35 3
# mutation 2 7  2 2  432  35 3
nonsynonymous SNV 2 5  2 1  322  25 2
synonymous SNV   2    1  11   1  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
chr20:48256324p.R9L1
chr20:48263529p.E387V1
chr20:48330202p.C158R1
chr20:48252856p.G311G1
chr20:48257081p.E139Q1
chr20:48263537p.R306G1
chr20:48253964p.H138H1
chr20:48257123p.T113T1
chr20:48263558p.D302N1
chr20:48256216p.T113N1

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 B4GALT5 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 B4GALT5

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

ACTR3,ATP11C,B4GALT5,BEND3,CBFB,CENPI,CORO1C,
CSE1L,DDX27,FAM83D,HIVEP2,MYBL2,PATL1,RNF114,
RQCD1,SF3B3,SOS1,STAU1,TRRAP,UBE2V1,YEATS2
AP4E1,ATP11A,B4GALT5,BICC1,CCND2,CHSY3,CPSF2,
EIF4G2,CCSER2,HIVEP2,KBTBD2,LRP12,MFAP3,PANX1,
PRRG1,RPS6KA3,SSH1,TAF13,TFDP1,TSHZ3,ZNF385D

ADNP,ASXL1,B4GALT5,ELMO2,ITCH,TTI1,KIF3B,
MAPRE1,NCOA3,NCOA6,PHF20,PLAGL2,PTPN1,RALGAPB,
RBL1,RPRD1B,STAU1,STK4,TTPAL,VAPB,ZNFX1
AAK1,SOWAHC,B4GALT1,B4GALT5,CEACAM5,CTNNA1,DSC2,
FLNB,GNA13,GNAQ,GPD2,GTPBP1,KIF16B,MICAL2,
OSBPL11,OXSR1,PDLIM5,RAPGEF2,SMCHD1,TCF7L2,TMEM65
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 B4GALT5


There's no related Drug.
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Cross referenced IDs for B4GALT5
* 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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