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 B4GALT6
Basic gene info.Gene symbolB4GALT6
Gene nameUDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 6
SynonymsB4Gal-T6|beta4Gal-T6
CytomapUCSC genome browser: 18q11
Genomic locationchr18 :29202208-29264686
Type of geneprotein-coding
RefGenesNM_004775.3,
Ensembl idENSG00000118276
DescriptionUDP-Gal:beta-GlcNAc beta-1,4-galactosyltransferase 6UDP-Gal:glucosylceramide beta-1,4-galactosyltransferaseUDP-galactose:beta-N-acetylglucosamine beta-1,4-galactosyltransferase 6beta-1,4-GalTase 6beta-1,4-galactosyltransferase 6beta4GalT-VI
Modification date20141207
dbXrefs MIM : 604017
HGNC : HGNC
Ensembl : ENSG00000118276
HPRD : 06808
Vega : OTTHUMG00000131980
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_B4GALT6
BioGPS: 9331
Gene Expression Atlas: ENSG00000118276
The Human Protein Atlas: ENSG00000118276
PathwayNCI Pathway Interaction Database: B4GALT6
KEGG: B4GALT6
REACTOME: B4GALT6
ConsensusPathDB
Pathway Commons: B4GALT6
MetabolismMetaCyc: B4GALT6
HUMANCyc: B4GALT6
RegulationEnsembl's Regulation: ENSG00000118276
miRBase: chr18 :29,202,208-29,264,686
TargetScan: NM_004775
cisRED: ENSG00000118276
ContextiHOP: B4GALT6
cancer metabolism search in PubMed: B4GALT6
UCL Cancer Institute: B4GALT6
Assigned class in ccmGDBC

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Phenotypic Information for B4GALT6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: B4GALT6
Familial Cancer Database: B4GALT6
* 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_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_PROTEINS
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: B4GALT6
MedGen: B4GALT6 (Human Medical Genetics with Condition)
ClinVar: B4GALT6
PhenotypeMGI: B4GALT6 (International Mouse Phenotyping Consortium)
PhenomicDB: B4GALT6

Mutations for B4GALT6
* 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
ovaryB4GALT6chr182925426229254282chr182929861729298637
pancreasB4GALT6chr182922860229228622B4GALT6chr182922966229229682
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 B4GALT6 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      1   3   1  
GAIN (# sample)          2   1  
LOSS (# sample)      1   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=40)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr18:29218688-29218688p.E169D3
chr18:29218625-29218625p.A190A2
chr18:29225417-29225417p.S124R2
chr18:29207071-29207071p.E264*2
chr18:29264323-29264325p.F22delF2
chr18:29225320-29225320p.K157E2
chr18:29264345-29264345p.L15L2
chr18:29210958-29210958p.R247H2
chr18:29206995-29206995p.G289V2
chr18:29246273-29246273p.I60V2

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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
# sample12 81 2 1  52   23 6
# mutation12 81 2 1  52   23 7
nonsynonymous SNV11 61 2    52    2 6
synonymous SNV 1 2    1       21 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
chr18:29225320p.K157E2
chr18:29206995p.G289V2
chr18:29218695p.A377D1
chr18:29205596p.D228N1
chr18:29210931p.K358N1
chr18:29205652p.M216V1
chr18:29210933p.R356S1
chr18:29225342p.G211G1
chr18:29205658p.I347I1
chr18:29210956p.R204H1

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 B4GALT6 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 B4GALT6

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

B4GALT6,BIVM,CCDC88A,CEP192,CEP76,ICA1L,TRAPPC8,
PABPC4L,PHYHIPL,RAVER2,RIOK3,RNF138,RNF138P1,SCML2,
SMCHD1,SPAST,TAF4B,TMOD2,TMX3,TRPC1,XKR5
ARHGAP42,AZI2,B4GALT6,C6orf120,CCDC50,CD164,CRYBG3,
DCBLD2,MICU3,FAM160B1,FBXL5,KIAA1715,NHLRC3,PPP3R1,
SLC25A16,SNTB2,TMED5,SLC35G1,TMEM55A,YIPF4,ZHX1

ATP1B1,B4GALT6,C18orf21,C18orf25,LINC00323,DSG2,EIF5A2,
ELP2,ESCO1,HRASLS,INO80C,INPP1,KIAA0040,TRAPPC8,
NAPG,RBBP8,RNF138,RPRD1A,SLC39A6,ZNF24,ZNF271P
ALS2,ANO6,AZIN1,B4GALT6,PXDC1,CACNB2,CDR2L,
CNTNAP4,CYP2U1,DDHD2,ECM2,FAM3C,GRIK2,KCTD3,
MGC45800,PAQR3,SFXN3,SGMS1,SLC2A12,SLC4A7,TPPP3
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 B4GALT6


There's no related Drug.
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Cross referenced IDs for B4GALT6
* 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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