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 MGAT5
Basic gene info.Gene symbolMGAT5
Gene namemannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase
SynonymsGNT-V|GNT-VA
CytomapUCSC genome browser: 2q21.3
Genomic locationchr2 :135011829-135212192
Type of geneprotein-coding
RefGenesNM_002410.4,
Ensembl idENSG00000152127
DescriptionN-acetylglucosaminyl-transferase Valpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase Aalpha-mannoside beta-1,6-N-acetylglucosaminyltransferaseglcNAc-T Vmannoside acetylglucosaminyltransferase 5
Modification date20141222
dbXrefs MIM : 601774
HGNC : HGNC
Ensembl : ENSG00000152127
HPRD : 03467
Vega : OTTHUMG00000131681
ProteinUniProt: Q09328
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MGAT5
BioGPS: 4249
Gene Expression Atlas: ENSG00000152127
The Human Protein Atlas: ENSG00000152127
PathwayNCI Pathway Interaction Database: MGAT5
KEGG: MGAT5
REACTOME: MGAT5
ConsensusPathDB
Pathway Commons: MGAT5
MetabolismMetaCyc: MGAT5
HUMANCyc: MGAT5
RegulationEnsembl's Regulation: ENSG00000152127
miRBase: chr2 :135,011,829-135,212,192
TargetScan: NM_002410
cisRED: ENSG00000152127
ContextiHOP: MGAT5
cancer metabolism search in PubMed: MGAT5
UCL Cancer Institute: MGAT5
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MGAT5 in cancer cell metabolism1. Lau KS, Dennis JW (2008) N-Glycans in cancer progression. Glycobiology 18: 750-760. go to article

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Phenotypic Information for MGAT5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MGAT5
Familial Cancer Database: MGAT5
* 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 601774; gene.
Orphanet
DiseaseKEGG Disease: MGAT5
MedGen: MGAT5 (Human Medical Genetics with Condition)
ClinVar: MGAT5
PhenotypeMGI: MGAT5 (International Mouse Phenotyping Consortium)
PhenomicDB: MGAT5

Mutations for MGAT5
* 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
pancreasMGAT5chr2135180259135180279MGAT5chr2135180871135180891
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 MGAT5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI738610CENPH115056850603468506183MGAT51504162135163960135164226
AA249270MGAT511412135207519135207659RUNX1T113328489297150392971654
BX647087MGAT58742135207140135207206MGAT57153012135206960135212192
M86029MGAT511592135157585135157743MRPL1416033864408143144081609
AF088006TUG11625223137155631372180MGAT56176372135156085135156105
BF802193MGAT511352135208384135208519KIF1B12743711043667610436988

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 # sample1111  1 2     111
GAIN (# sample)1111  1 1       1
LOSS (# sample)        1     11 
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=79)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=2)
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
chr2:135180419-135180419p.H575Y3
chr2:135107416-135107416p.E385K3
chr2:135199357-135199357p.P633Q2
chr2:135012008-135012008p.Q12*2
chr2:135028017-135028017p.E101V2
chr2:135076304-135076304p.L189L2
chr2:135028028-135028028p.D105H2
chr2:135012017-135012017p.G15S2
chr2:135028123-135028123p.?2
chr2:135012161-135012161p.E63K2

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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
# sample13 131 1 51 1151  69 10
# mutation13 131 1 51 1171  611 13
nonsynonymous SNV12 121 1 31 961  59 10
synonymous SNV 1 1    2  21   12 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
chr2:135107416p.E385K3
chr2:135012017p.G15S2
chr2:135076256p.T680T1
chr2:135180413p.Q12E1
chr2:135012008p.V146A1
chr2:135099177p.G275E1
chr2:135206232p.K485N1
chr2:135012113p.R500R1
chr2:135107438p.A687A1
chr2:135076297p.Q12R1

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 MGAT5 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 MGAT5

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

ASXL2,BIRC6,ERCC6L2,CCNT1,EXOC6B,GTF2A1,LOC151162,
MAP3K2,MGAT5,NBEAL1,PRKAR2A,RAD54L2,RC3H2,REST,
RIF1,STRN,TGFBRAP1,TRIP12,UBR4,ZNF641,ZNF699
ASH1L,BIRC6,BRWD3,PRR14L,CCNT1,CLCN3,CNOT1,
DPY19L3,EP300,FAM168A,MGAT5,MYO9A,NF1,NR2C2,
PAFAH1B2,REST,VPS13B,WDFY3,ZDHHC20,ZKSCAN8,ZNF81

ASXL2,BIRC6,CCNT1,DDI2,IGF2R,KIAA0754,LOC151162,
MBD5,MFHAS1,MGAT5,MSI2,PROX1,RAD54L2,REST,
SERINC5,STRN,TGFBRAP1,TRIM44,TRIO,UHMK1,ZKSCAN1
AAK1,AKAP13,BMP2K,C10orf12,SPECC1L,DIP2B,EGFR,
FOXJ3,KDM5A,LCOR,LMTK2,LOC151162,MGAT5,MICAL2,
MICAL3,NBPF1,NCOA2,RAPGEF2,SMCHD1,TRPM6,ZMYND8
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 MGAT5


There's no related Drug.
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Cross referenced IDs for MGAT5
* 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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