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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for MGAT4B |
Basic gene info. | Gene symbol | MGAT4B |
Gene name | mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme B | |
Synonyms | GNT-IV|GNT-IVB | |
Cytomap | UCSC genome browser: 5q35 | |
Genomic location | chr5 :179224597-179233952 | |
Type of gene | protein-coding | |
RefGenes | NM_014275.4, NM_054013.3, | |
Ensembl id | ENSG00000161013 | |
Description | N-acetylglucosaminyltransferase IVbN-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase IVbUDP-N-acetylglucosamine: alpha-1,3-D-mannoside beta-1,4-N-acetylglucosaminyltransferase IVUDP-N-acetylglucosamine: alpha-1,3-D-mannoside beta- | |
Modification date | 20141207 | |
dbXrefs | MIM : 604561 | |
HGNC : HGNC | ||
Ensembl : ENSG00000161013 | ||
HPRD : 05190 | ||
Vega : OTTHUMG00000130912 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_MGAT4B | |
BioGPS: 11282 | ||
Gene Expression Atlas: ENSG00000161013 | ||
The Human Protein Atlas: ENSG00000161013 | ||
Pathway | NCI Pathway Interaction Database: MGAT4B | |
KEGG: MGAT4B | ||
REACTOME: MGAT4B | ||
ConsensusPathDB | ||
Pathway Commons: MGAT4B | ||
Metabolism | MetaCyc: MGAT4B | |
HUMANCyc: MGAT4B | ||
Regulation | Ensembl's Regulation: ENSG00000161013 | |
miRBase: chr5 :179,224,597-179,233,952 | ||
TargetScan: NM_014275 | ||
cisRED: ENSG00000161013 | ||
Context | iHOP: MGAT4B | |
cancer metabolism search in PubMed: MGAT4B | ||
UCL Cancer Institute: MGAT4B | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for MGAT4B(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: MGAT4B |
Familial Cancer Database: MGAT4B |
* 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 |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: MGAT4B |
MedGen: MGAT4B (Human Medical Genetics with Condition) | |
ClinVar: MGAT4B | |
Phenotype | MGI: MGAT4B (International Mouse Phenotyping Consortium) |
PhenomicDB: MGAT4B |
Mutations for MGAT4B |
* 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 MGAT4B 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 |
BE089562 | MALAT1 | 9 | 167 | 11 | 65268150 | 65268310 | MGAT4B | 163 | 389 | 5 | 179225193 | 179225566 | |
AW793754 | MGAT4B | 44 | 169 | 5 | 179227905 | 179228410 | MGAT4B | 162 | 235 | 5 | 179225533 | 179225943 |
Other DBs for Structural Variants |
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Copy 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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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=41) | (# total SNVs=7) |
(# total SNVs=2) | (# 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 |
chr5:179226507-179226507 | p.A362V | 3 |
chr5:179228604-179228604 | p.K140T | 2 |
chr5:179225598-179225598 | p.? | 2 |
chr5:179225986-179225986 | p.T444P | 2 |
chr5:179228969-179228969 | p.G48V | 2 |
chr5:179226037-179226037 | p.H427N | 2 |
chr5:179228441-179228441 | p.V166M | 1 |
chr5:179225552-179225552 | p.D476D | 1 |
chr5:179229025-179229025 | p.G29G | 1 |
chr5:179226129-179226129 | p.? | 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 | 1 | 2 |   | 6 | 2 |   | 2 |   | 2 |   |   | 3 | 1 | 1 |   |   | 1 | 3 |   | 5 |
# mutation | 1 | 2 |   | 6 | 1 |   | 2 |   | 2 |   |   | 4 | 1 | 1 |   |   | 1 | 3 |   | 7 |
nonsynonymous SNV |   | 2 |   | 5 | 1 |   | 2 |   | 1 |   |   | 4 | 1 | 1 |   |   |   | 3 |   | 5 |
synonymous SNV | 1 |   |   | 1 |   |   |   |   | 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 |
chr5:179225986 | p.T444P,MGAT4B | 3 |
chr5:179226075 | p.R541C,MGAT4B | 1 |
chr5:179228606 | p.M295T,MGAT4B | 1 |
chr5:179225415 | p.E245D,MGAT4B | 1 |
chr5:179226099 | p.D513N,MGAT4B | 1 |
chr5:179228625 | p.R244Q,MGAT4B | 1 |
chr5:179225513 | p.E496G,MGAT4B | 1 |
chr5:179226297 | p.R242C,MGAT4B | 1 |
chr5:179228838 | p.D489D,MGAT4B | 1 |
chr5:179225515 | p.S241C,MGAT4B | 1 |
Other DBs for Point Mutations |
Copy Number for MGAT4B 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 MGAT4B |
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 |
ATAD3A,DAZAP1,DDX41,ESRRA,FBXW5,GRK6,IFRD2, IRAK1,LOC388955,LTBR,MGAT1,MGAT4B,MXD3,NHP2, NOP16,POLD1,PRELID1,RPS6KA4,SMG5,TSPAN17,ZNF598 | BTBD2,EMC10,C9orf16,CHID1,CHPF,CLN6,COPE, DTYMK,H2AFX,LYPLA2,MAZ,MFSD10,MGAT4B,PLSCR3, PPP1CA,RHBDD3,RPUSD1,SIRT6,TARBP2,TOR2A,YIF1B |
ANO9,AXIN1,BLCAP,CCDC64B,CLCN2,DAGLA,EPS8L2, ESRRA,GPR35,GTF2IRD1,IHH,INPP5J,MGAT4B,MOGAT3, NECAB3,PPDPF,PRSS8,PYGB,SCAP,SQSTM1,TPRN | ACSF3,CBLC,CTSD,DHRS11,EPN1,ESRRA,GPR35, HPS1,ITPKA,KIAA1522,KLC4,MAP3K11,MGAT4B,NGEF, PDLIM1,PFKL,PRKCZ,SPINT1,TMC4,USH1C,VIPR1 |
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 MGAT4B |
There's no related Drug. |
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Cross referenced IDs for MGAT4B |
* 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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