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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for B4GALT4 |
Basic gene info. | Gene symbol | B4GALT4 |
Gene name | UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4 | |
Synonyms | B4Gal-T4|beta4Gal-T4 | |
Cytomap | UCSC genome browser: 3q13.3 | |
Genomic location | chr3 :118930588-118959752 | |
Type of gene | protein-coding | |
RefGenes | NM_003778.3, NM_212543.1, | |
Ensembl id | ENSG00000121578 | |
Description | UDP-Gal:beta-GlcNAc beta-1,4-galactosyltransferase 4UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase 4UDP-galactose:beta-N-acetylglucosamine beta-1,4-galactosyltransferase 4beta-1,4-GalTase 4beta-1,4-galactosyltransferase 4beta-N-acetylglucosaminyl | |
Modification date | 20141207 | |
dbXrefs | MIM : 604015 | |
HGNC : HGNC | ||
Ensembl : ENSG00000121578 | ||
HPRD : 04930 | ||
Vega : OTTHUMG00000159358 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_B4GALT4 | |
BioGPS: 8702 | ||
Gene Expression Atlas: ENSG00000121578 | ||
The Human Protein Atlas: ENSG00000121578 | ||
Pathway | NCI Pathway Interaction Database: B4GALT4 | |
KEGG: B4GALT4 | ||
REACTOME: B4GALT4 | ||
ConsensusPathDB | ||
Pathway Commons: B4GALT4 | ||
Metabolism | MetaCyc: B4GALT4 | |
HUMANCyc: B4GALT4 | ||
Regulation | Ensembl's Regulation: ENSG00000121578 | |
miRBase: chr3 :118,930,588-118,959,752 | ||
TargetScan: NM_003778 | ||
cisRED: ENSG00000121578 | ||
Context | iHOP: B4GALT4 | |
cancer metabolism search in PubMed: B4GALT4 | ||
UCL Cancer Institute: B4GALT4 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for B4GALT4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: B4GALT4 |
Familial Cancer Database: B4GALT4 |
* 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 B4GALT4 |
* 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 |
- Statistics for Tissue and Mutation type | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
pancreas | B4GALT4 | chr3 | 118935571 | 118935591 | chr3 | 126840990 | 126841010 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows B4GALT4 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 |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   |   | 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=23) | (# total SNVs=10) |
(# total SNVs=1) | (# total SNVs=0) |
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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 |
chr3:118945809-118945809 | p.G111G | 3 |
chr3:118945796-118945796 | p.Q116E | 2 |
chr3:118948792-118948792 | p.H52R | 2 |
chr3:118931456-118931456 | p.V325V | 2 |
chr3:118931498-118931498 | p.V311V | 2 |
chr3:118937520-118937520 | p.G258G | 2 |
chr3:118931416-118931416 | p.D339H | 1 |
chr3:118937531-118937531 | p.G255* | 1 |
chr3:118943002-118943002 | p.H193Y | 1 |
chr3:118931425-118931425 | p.I336V | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   | 3 |   | 4 |   |   |   |   | 1 |   |   | 3 | 4 |   |   |   | 2 | 6 |   | 3 |
# mutation |   | 3 |   | 4 |   |   |   |   | 1 |   |   | 4 | 4 |   |   |   | 2 | 6 |   | 3 |
nonsynonymous SNV |   | 1 |   | 2 |   |   |   |   | 1 |   |   | 2 | 3 |   |   |   | 1 | 4 |   | 3 |
synonymous SNV |   | 2 |   | 2 |   |   |   |   |   |   |   | 2 | 1 |   |   |   | 1 | 2 |   |   |
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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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 |
chr3:118937520 | p.G258G,B4GALT4 | 3 |
chr3:118931416 | p.R301W,B4GALT4 | 1 |
chr3:118942945 | p.N105H,B4GALT4 | 1 |
chr3:118948710 | p.G294G,B4GALT4 | 1 |
chr3:118931440 | p.L90L,B4GALT4 | 1 |
chr3:118943002 | p.L263L,B4GALT4 | 1 |
chr3:118948741 | p.P82A,B4GALT4 | 1 |
chr3:118931514 | p.S79S,B4GALT4 | 1 |
chr3:118943051 | p.F249F,B4GALT4 | 1 |
chr3:118948756 | p.T69M,B4GALT4 | 1 |
Other DBs for Point Mutations |
Copy Number for B4GALT4 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 B4GALT4 |
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)) |
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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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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 |
ATG3,ATP2C1,B4GALT4,TIMMDC1,CALU,COPG1,DIRC2, GSK3B,KPNA1,KPNA4,NAA50,OSBPL11,POLQ,RAB7A, RPN1,SEC22A,SEC61A1,SNX4,TBC1D23,TFG,TMEM39A | B4GALT4,XXYLT1,CHEK2,DCLRE1B,DNAJB11,DSN1,EXT1, GGTA1P,HDAC8,HSP90B1,IFT57,LPCAT1,MESDC2,PITPNA, QPCT,SETD8,STX6,TOR1A,TOR1B,UMPS,XPO6 | ||||
ATP2A3,B3GNT6,B4GALT4,BCAS1,C3orf52,SMIM14,CAMK2D, CAPN5,CAPN9,FAM174B,FAM83E,FCGBP,GALNT12,GALNT7, LRRIQ4,NUDT16,PLD1,SCNN1A,SIDT1,SLC22A23,TMEM61 | AKAP9,APPL2,B4GALT4,BCL2L11,GALNT7,GCC2,LGR4, NR3C2,NUMB,PIK3CB,PIP5K1B,POF1B,PPAPDC2,PRKCD, SLC35B3,STYK1,SYAP1,TAOK3,TRIM36,TSPAN3,VDR |
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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for B4GALT4 |
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 4 | approved; nutraceutical | N-Acetyl-D-glucosamine |
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Cross referenced IDs for B4GALT4 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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