Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	MGAT5
	Gene name	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase
	Synonyms	GNT-V\|GNT-VA
	Cytomap	UCSC genome browser: 2q21.3
	Genomic location	chr2 :135011829-135212192
	Type of gene	protein-coding
	RefGenes	NM_002410.4,
	Ensembl id	ENSG00000152127
	Description	N-acetylglucosaminyl-transferase Valpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase Aalpha-mannoside beta-1,6-N-acetylglucosaminyltransferaseglcNAc-T Vmannoside acetylglucosaminyltransferase 5
	Modification date	20141222
dbXrefs	MIM : 601774
	HGNC : HGNC
	Ensembl : ENSG00000152127
	HPRD : 03467
	Vega : OTTHUMG00000131681
Protein	UniProt: Q09328 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MGAT5
	BioGPS: 4249
	Gene Expression Atlas: ENSG00000152127
	The Human Protein Atlas: ENSG00000152127
Pathway	NCI Pathway Interaction Database: MGAT5
	KEGG: MGAT5
	REACTOME: MGAT5
	ConsensusPathDB
	Pathway Commons: MGAT5
Metabolism	MetaCyc: MGAT5
	HUMANCyc: MGAT5
Regulation	Ensembl's Regulation: ENSG00000152127
	miRBase: chr2 :135,011,829-135,212,192
	TargetScan: NM_002410
	cisRED: ENSG00000152127
Context	iHOP: MGAT5
	cancer metabolism search in PubMed: MGAT5
	UCL Cancer Institute: MGAT5
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MGAT5 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM	601774; gene.
Orphanet
Disease	KEGG Disease: MGAT5
	MedGen: MGAT5 (Human Medical Genetics with Condition)
	ClinVar: MGAT5
Phenotype	MGI: MGAT5 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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	MGAT5	chr2	135180259	135180279	MGAT5	chr2	135180871	135180891

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 MGAT5 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
AI738610	CENPH	1	150	5	68506034	68506183	MGAT5	150	416	2	135163960	135164226
AA249270	MGAT5	1	141	2	135207519	135207659	RUNX1T1	133	284	8	92971503	92971654
BX647087	MGAT5	8	74	2	135207140	135207206	MGAT5	71	5301	2	135206960	135212192
M86029	MGAT5	1	159	2	135157585	135157743	MRPL14	160	338	6	44081431	44081609
AF088006	TUG1	1	625	22	31371556	31372180	MGAT5	617	637	2	135156085	135156105
BF802193	MGAT5	1	135	2	135208384	135208519	KIF1B	127	437	1	10436676	10436988

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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	1	1	1			1		2						1	1	1
GAIN (# sample)	1	1	1	1			1		1								1
LOSS (# sample)									1						1	1

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

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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Somatic 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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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
chr2:135180419-135180419	p.H575Y	3
chr2:135107416-135107416	p.E385K	3
chr2:135012194-135012194	p.A74T	2
chr2:135102621-135102621	p.S366S	2
chr2:135180384-135180384	p.Q563R	2
chr2:135206337-135206337	p.G715G	2
chr2:135199357-135199357	p.P633Q	2
chr2:135012008-135012008	p.Q12*	2
chr2:135028017-135028017	p.E101V	2
chr2:135076304-135076304	p.L189L	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	3		13	1		1		5	1		11	5	1			6	9		10
# mutation	1	3		13	1		1		5	1		11	7	1			6	11		13
nonsynonymous SNV	1	2		12	1		1		3	1		9	6	1			5	9		10
synonymous SNV		1		1					2			2	1				1	2		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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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
chr2:135107416	p.E385K	3
chr2:135012017	p.G15S	2
chr2:135185972	p.F607I	1
chr2:135093810	p.P40P	1
chr2:135206361	p.E191Q	1
chr2:135012073	p.Y391C	1
chr2:135102586	p.C609C	1
chr2:135160678	p.L46M	1
chr2:135075138	p.E191D	1
chr2:135185973	p.A392V	1

Other 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

Copy 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

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.

: Open all plots for all cancer types

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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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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