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 B3GNT9
Basic gene info.Gene symbolB3GNT9
Gene nameUDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9
Synonyms-
CytomapUCSC genome browser: 16q22.1
Genomic locationchr16 :67182004-67184902
Type of geneprotein-coding
RefGenesNM_033309.2,
Ensembl idENSG00000237172
DescriptionBGnT-9beta-1,3-Gn-T9beta-1,3-N-acetylglucosaminyltransferase 9beta-1,3-galactosyltransferase-related proteinbeta3Gn-T9
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000237172
HPRD : 14651
Vega : OTTHUMG00000173315
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_B3GNT9
BioGPS: 84752
Gene Expression Atlas: ENSG00000237172
The Human Protein Atlas: ENSG00000237172
PathwayNCI Pathway Interaction Database: B3GNT9
KEGG: B3GNT9
REACTOME: B3GNT9
ConsensusPathDB
Pathway Commons: B3GNT9
MetabolismMetaCyc: B3GNT9
HUMANCyc: B3GNT9
RegulationEnsembl's Regulation: ENSG00000237172
miRBase: chr16 :67,182,004-67,184,902
TargetScan: NM_033309
cisRED: ENSG00000237172
ContextiHOP: B3GNT9
cancer metabolism search in PubMed: B3GNT9
UCL Cancer Institute: B3GNT9
Assigned class in ccmGDBC

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Phenotypic Information for B3GNT9(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: B3GNT9
Familial Cancer Database: B3GNT9
* 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: B3GNT9
MedGen: B3GNT9 (Human Medical Genetics with Condition)
ClinVar: B3GNT9
PhenotypeMGI: B3GNT9 (International Mouse Phenotyping Consortium)
PhenomicDB: B3GNT9

Mutations for B3GNT9
* 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 B3GNT9 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
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=23)
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
chr16:67183675-67183675p.N238K2
chr16:67183690-67183690p.F233F2
chr16:67183705-67183705p.G228G2
chr16:67183243-67183243p.P382P2
chr16:67184131-67184131p.R86R2
chr16:67183379-67183379p.R337H2
chr16:67183643-67183643p.A249V1
chr16:67183812-67183812p.L193M1
chr16:67184225-67184225p.A55V1
chr16:67183399-67183399p.P330P1

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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 71    1  1   15 6
# mutation22 72    1  1   15 7
nonsynonymous SNV21 51       1    2 4
synonymous SNV 1 21    1      13 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
chr16:67183690p.R86R2
chr16:67184131p.F233F2
chr16:67183705p.R151C1
chr16:67184165p.A297A1
chr16:67183468p.N101T1
chr16:67183755p.A287T1
chr16:67183498p.R262W1
chr16:67183798p.T77M1
chr16:67183530p.V257I1
chr16:67183810p.P75L1

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 B3GNT9 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 B3GNT9

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

B3GNT9,CERCAM,CHPF,COL1A1,COL1A2,COL3A1,COL5A1,
COPZ2,FKBP7,GLG1,HHIPL1,LEPRE1,MMP2,MRC2,
PCDHGC3,PDGFRL,PPIC,SLC12A4,SMPD1,SPARC,TPST1
B3GNT9,KIAA0930,CALR,CAPN5,CD276,CERCAM,CHST14,
CKAP4,CLEC11A,CNPY4,FAM109B,FKBP10,GNA15,LEPREL2,
LTBP3,MGAT4B,P4HA2,PCOLCE,LEPREL4,TIMP1,TP53I3

ARMCX2,CLMP,B3GNT9,CHST3,COL3A1,COL6A1,COPZ2,
EFS,EHD2,GLI3,GPX8,KIAA1462,LAMB2,LEPRE1,
LOXL1,MRC2,PLXDC2,TCEAL3,TPST1,TSHZ3,ZBTB47
ATP8B2,B3GNT9,BACE1,CERCAM,CHST14,COL18A1,COL5A2,
COL6A3,FAM120C,FKBP10,HDAC7,HHIPL1,LEPRE1,LEPREL2,
MAN1C1,MXRA8,NCKAP5L,NLGN2,RPS6KA2,SLC41A1,SRGAP2
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 B3GNT9


There's no related Drug.
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Cross referenced IDs for B3GNT9
* 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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