Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 MGAT4A
Basic gene info.Gene symbolMGAT4A
Gene namemannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A
SynonymsGNT-IV|GNT-IVA|GnT-4a
CytomapUCSC genome browser: 2q12
Genomic locationchr2 :99235568-99347589
Type of geneprotein-coding
RefGenesNM_001160154.1,
NM_012214.2,
Ensembl idENSG00000071073
DescriptionN-acetylglucosaminyltransferase IVaN-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase IVaUDP-GlcNAc:a-1,3-D-mannoside b-1,4-acetylglucosaminyltransferase IVUDP-N-acetylglucosamine: alpha-1,3-D-mannoside beta-1,4-N-acetylglucosaminy
Modification date20141207
dbXrefs MIM : 604623
HGNC : HGNC
Ensembl : ENSG00000071073
HPRD : 06860
Vega : OTTHUMG00000130563
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MGAT4A
BioGPS: 11320
Gene Expression Atlas: ENSG00000071073
The Human Protein Atlas: ENSG00000071073
PathwayNCI Pathway Interaction Database: MGAT4A
KEGG: MGAT4A
REACTOME: MGAT4A
ConsensusPathDB
Pathway Commons: MGAT4A
MetabolismMetaCyc: MGAT4A
HUMANCyc: MGAT4A
RegulationEnsembl's Regulation: ENSG00000071073
miRBase: chr2 :99,235,568-99,347,589
TargetScan: NM_001160154
cisRED: ENSG00000071073
ContextiHOP: MGAT4A
cancer metabolism search in PubMed: MGAT4A
UCL Cancer Institute: MGAT4A
Assigned class in ccmGDBC

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Phenotypic Information for MGAT4A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MGAT4A
Familial Cancer Database: MGAT4A
* 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: MGAT4A
MedGen: MGAT4A (Human Medical Genetics with Condition)
ClinVar: MGAT4A
PhenotypeMGI: MGAT4A (International Mouse Phenotyping Consortium)
PhenomicDB: MGAT4A

Mutations for MGAT4A
* 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
ovaryMGAT4Achr29929710499297124MGAT4Achr29931062899310648
prostateMGAT4Achr29929029399290293ACSL3chr2223803266223803266
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 MGAT4A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AU253288AUTS21931176963778269638074MGAT4A30662529923904399239368

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        2        
GAIN (# sample)        2        
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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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=30)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=4)
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
chr2:99251711-99251711p.R481Q4
chr2:99256692-99256692p.?2
chr2:99260500-99260500p.A302A2
chr2:99256595-99256595p.Q373fs*91
chr2:99294774-99294774p.K85K1
chr2:99271967-99271967p.N239H1
chr2:99342708-99342708p.G30R1
chr2:99279632-99279632p.V138V1
chr2:99256673-99256676p.Q346fs*351
chr2:99294780-99294780p.L83F1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 7  1 3  221  112 7
# mutation12 7  1 3  221  112 7
nonsynonymous SNV1  4    3  221  81 6
synonymous SNV 2 3  1         31 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
chr2:99251711p.R353Q,MGAT4A3
chr2:99260500p.A174A,MGAT4A2
chr2:99342746p.E267D,MGAT4A1
chr2:99272821p.E39D,MGAT4A1
chr2:99279639p.L28L,MGAT4A1
chr2:99256314p.P265S,MGAT4A1
chr2:99272830p.V10V,MGAT4A1
chr2:99291500p.H261Y,MGAT4A1
chr2:99256384p.S8L,MGAT4A1
chr2:99272887p.L201L,MGAT4A1

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 MGAT4A 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 MGAT4A

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

AFF3,SMIM14,CDYL2,CLCN3,FAM63B,FAM73A,FOXA1,
FRY,GCC2,GLUD2,HCAR1,KIAA1244,LCOR,MGAT4A,
PCYOX1,RASEF,SPRED2,UBR1,WDFY3,XIAP,ZSWIM6
AFTPH,AP1AR,EDEM1,GSTCD,HOOK1,MGAT4A,MOB1B,
MYO6,RALGPS2,PTBP3,SAMD12,SLC11A2,SS18,TMEM67,
TMEM87B,ZNF107,ZNF260,ZNF439,ZNF738,ZNF860,ZNRF2

ACSS2,B3GALT5,CEACAM20,DLL4,EML4,FZD5,GNA11,
SLC52A1,KRT20,LRRC1,MAP3K15,MGAT4A,NR5A2,PAG1,
PHLPP2,PLS1,PPM1B,RBM47,SEMA6A,SLC9A3R1,TP53INP2
ACSL5,ANKS4B,ANO10,LINC00483,C1orf106,CXADR,DOLPP1,
TMEM236,FMO4,HECTD3,KALRN,KIAA0247,LASP1,MGAT4A,
MPP5,PHLPP2,PSEN1,PTPRJ,RETSAT,SLC41A2,TRIM36
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 MGAT4A


There's no related Drug.
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Cross referenced IDs for MGAT4A
* 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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