|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for B4GALT3 |
Basic gene info. | Gene symbol | B4GALT3 |
Gene name | UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3 | |
Synonyms | beta4Gal-T3 | |
Cytomap | UCSC genome browser: 1q21-q23 | |
Genomic location | chr1 :161141099-161147758 | |
Type of gene | protein-coding | |
RefGenes | NM_001199873.1, NM_001199874.1,NM_003779.3, | |
Ensembl id | ENSG00000158850 | |
Description | UDP-Gal:beta-GlcNAc beta-1,4-galactosyltransferase 3UDP-galactose:beta-N-acetylglucosamine beta-1,4-galactosyltransferase 3b4Gal-T3beta-1,4-GalTase 3beta-1,4-galactosyltransferase 3beta-N-acetylglucosaminyl-glycolipid beta-1,4-galactosyltransferase 3 | |
Modification date | 20141207 | |
dbXrefs | MIM : 604014 | |
HGNC : HGNC | ||
Ensembl : ENSG00000158850 | ||
HPRD : 04929 | ||
Vega : OTTHUMG00000034348 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_B4GALT3 | |
BioGPS: 8703 | ||
Gene Expression Atlas: ENSG00000158850 | ||
The Human Protein Atlas: ENSG00000158850 | ||
Pathway | NCI Pathway Interaction Database: B4GALT3 | |
KEGG: B4GALT3 | ||
REACTOME: B4GALT3 | ||
ConsensusPathDB | ||
Pathway Commons: B4GALT3 | ||
Metabolism | MetaCyc: B4GALT3 | |
HUMANCyc: B4GALT3 | ||
Regulation | Ensembl's Regulation: ENSG00000158850 | |
miRBase: chr1 :161,141,099-161,147,758 | ||
TargetScan: NM_001199873 | ||
cisRED: ENSG00000158850 | ||
Context | iHOP: B4GALT3 | |
cancer metabolism search in PubMed: B4GALT3 | ||
UCL Cancer Institute: B4GALT3 | ||
Assigned class in ccmGDB | C |
Top |
Phenotypic Information for B4GALT3(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: B4GALT3 |
Familial Cancer Database: B4GALT3 |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_PROTEINS REACTOME_METABOLISM_OF_CARBOHYDRATES |
Mutations for B4GALT3 |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows B4GALT3 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
Other DBs for Structural Variants |
Top |
Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=30) | (# total SNVs=8) |
(# total SNVs=1) | (# total SNVs=1) |
Top |
Top 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 position | Mutation(aa) | Unique sampleID count |
chr1:161145720-161145720 | p.P44L | 2 |
chr1:161145756-161145756 | p.R32Q | 2 |
chr1:161141721-161141721 | p.R356H | 2 |
chr1:161143511-161143511 | p.P229P | 2 |
chr1:161145843-161145843 | p.R3Q | 2 |
chr1:161143749-161143749 | p.H194Y | 2 |
chr1:161145604-161145604 | p.L83I | 2 |
chr1:161143801-161143801 | p.N176N | 1 |
chr1:161141693-161141693 | p.F365F | 1 |
chr1:161145718-161145718 | p.T45P | 1 |
Top |
SNV Counts per Each Loci in TCGA data |
|
Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   |   | 1 | 7 |   |   |   |   |   |   | 1 | 1 | 4 |   |   |   | 2 | 5 |   | 10 |
# mutation |   |   | 1 | 7 |   |   |   |   |   |   | 1 | 1 | 4 |   |   |   | 2 | 5 |   | 12 |
nonsynonymous SNV |   |   | 1 | 7 |   |   |   |   |   |   |   | 1 | 4 |   |   |   | 1 | 2 |   | 8 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   | 1 | 3 |   | 4 |
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]) |
Top |
Top 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 Position | Mutation(aa) | Unique sampleID count |
chr1:161141721 | p.R356H,B4GALT3 | 3 |
chr1:161145604 | p.L83F,B4GALT3 | 2 |
chr1:161143511 | p.P229P,B4GALT3 | 2 |
chr1:161145641 | p.R347Q,B4GALT3 | 1 |
chr1:161143694 | p.A126D,B4GALT3 | 1 |
chr1:161145718 | p.D345D,B4GALT3 | 1 |
chr1:161141748 | p.R122R,B4GALT3 | 1 |
chr1:161143746 | p.T323T,B4GALT3 | 1 |
chr1:161145756 | p.R122C,B4GALT3 | 1 |
chr1:161141753 | p.P301S,B4GALT3 | 1 |
Other DBs for Point Mutations |
Copy Number for B4GALT3 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] |
Top |
Gene Expression for B4GALT3 |
Gene 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. |
Differential 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)) |
Top |
CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
Top |
Gene-Gene Network Information |
Co-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 |
B4GALT3,DEDD,DUSP12,EFNA4,F11R,FLAD1,MSTO1, NDUFS2,NIT1,PPOX,PRCC,PVRL4,SCAMP3,SDHC, SSR2,TOMM40L,UBE2Q1,UBQLN4,UFC1,USF1,USP21 | APH1A,B4GALT3,SWSAP1,DALRD3,DHRS13,EFNA3,EFNA4, ELMO3,KIF22,LOC92659,NMRAL1,PGAP2,PPAP2C,PRR19, PRSS8,RAB25,SAMD10,TMEM125,TMEM198,TRIM28,TSEN54 | ||||
ADIPOR1,APH1A,B4GALT3,C1orf43,DAP3,DEDD,DUSP12, FLAD1,HAX1,JTB,LYSMD1,MRPL9,MRPS14,PPOX, PYCR2,LAMTOR2,SCAMP3,UBE2Q1,UBQLN4,USP21,VPS72 | ADCK2,B4GALT3,VWA9,DALRD3,DCAF12,DDX41,DUS1L, EDEM2,GSS,ICAM3,LIME1,MAPKAPK3,NGLY1,RAB25, RNASET2,RPIA,SLC35C2,SMAGP,TPST2,TRABD,YDJC |
Co-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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for B4GALT3 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00141 | UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3 | approved; nutraceutical | N-Acetyl-D-glucosamine |
Top |
Cross referenced IDs for B4GALT3 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |