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 MGAT4C

Basic gene info.	Gene symbol	MGAT4C
	Gene name	MGAT4 family, member C
	Synonyms	GNTIVH\|HGNT-IV-H
	Cytomap	UCSC genome browser: 12q21
	Genomic location	chr12 :86373036-87232681
	Type of gene	protein-coding
	RefGenes	NM_013244.3,
	Ensembl id	ENSG00000182050
	Description	N-acetylglucosaminyltransferase IV homologN-acetylglucosaminyltransferase IVcN-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase IVcUDP-N-acetylglucosamine: alpha-1,3-D-mannoside beta-1,4-N-acetylglucosaminyltransferase IVcUDP-N-ac
	Modification date	20141207
dbXrefs	MIM : 607385
	HGNC : HGNC
	HPRD : 09575
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MGAT4C
	BioGPS: 25834
	Gene Expression Atlas: ENSG00000182050
	The Human Protein Atlas: ENSG00000182050
Pathway	NCI Pathway Interaction Database: MGAT4C
	KEGG: MGAT4C
	REACTOME: MGAT4C
	ConsensusPathDB
	Pathway Commons: MGAT4C
Metabolism	MetaCyc: MGAT4C
	HUMANCyc: MGAT4C
Regulation	Ensembl's Regulation: ENSG00000182050
	miRBase: chr12 :86,373,036-87,232,681
	TargetScan: NM_013244
	cisRED: ENSG00000182050
Context	iHOP: MGAT4C
	cancer metabolism search in PubMed: MGAT4C
	UCL Cancer Institute: MGAT4C
Assigned class in ccmGDB	C

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Phenotypic Information for MGAT4C(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MGAT4C
	Familial Cancer Database: MGAT4C

* 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
Orphanet
Disease	KEGG Disease: MGAT4C
	MedGen: MGAT4C (Human Medical Genetics with Condition)
	ClinVar: MGAT4C
Phenotype	MGI: MGAT4C (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MGAT4C

Mutations for MGAT4C

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
ovary	MGAT4C	chr12	86423776	86423796		chr12	90706928	90706948
ovary	MGAT4C	chr12	86556010	86556030	MGAT4C	chr12	86556060	86556080
ovary	MGAT4C	chr12	86849729	86849749		chr23	11732318	11732338
ovary	MGAT4C	chr12	86864799	86864819	MATN2	chr8	99005757	99005777
ovary	MGAT4C	chr12	87050205	87050225	MGAT4C	chr12	87043251	87043271
pancreas	MGAT4C	chr12	86387036	86387056	LRRIQ1	chr12	85536003	85536023
pancreas	MGAT4C	chr12	86523315	86523335	MGAT4C	chr12	86523626	86523646
pancreas	MGAT4C	chr12	86662537	86662557	MGAT4C	chr12	86666592	86666612
pancreas	MGAT4C	chr12	86782188	86782208	MGAT4C	chr12	86748474	86748494
pancreas	MGAT4C	chr12	87028823	87028843	MGAT4C	chr12	87081551	87081571

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 MGAT4C 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
AB024730	LOC151009	1	92	2	111140898	111140989	MGAT4C	91	2535	12	86372524	87232645
BU567782	MGAT4C	4	157	12	86650016	86650169	LOC400655	145	748	18	70826776	70840208
T08449	MGAT4C	1	51	12	87168299	87168349	GRM4	46	404	6	33990485	33992189
AB024729	LOC151009	1	92	2	111140898	111140989	MGAT4C	91	2655	12	86372524	87232645
BI002606	LDLRAD2	20	201	1	22148743	22148924	MGAT4C	194	295	12	86588704	86588805

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	6	3									2			1		1	1
GAIN (# sample)	5	2									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=11

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=92)	Stat. for Synonymous SNVs (# total SNVs=16)

Stat. for Deletions (# total SNVs=4)	Stat. for Insertions (# total SNVs=1)

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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
chr12:86373294-86373294	p.D404N	6
chr12:86374059-86374059	p.R149C	6
chr12:86374058-86374058	p.R149H	5
chr12:86373821-86373821	p.R228Q	4
chr12:86373542-86373542	p.T321M	4
chr12:86373822-86373822	p.R228*	3
chr12:86373909-86373909	p.R199C	3
chr12:86377377-86377377	p.F73F	3
chr12:86373279-86373279	p.G409*	2
chr12:86377313-86377313	p.L95L	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=5

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	1	16	2		2		3		1	16	5	3		2	20	6		12
# mutation	1	2	2	13	2		2		3		1	14	6	3		2	21	8		14
nonsynonymous SNV	1	2	2	12	2		1		2		1	11	5	2		2	15	7		12
synonymous SNV				1			1		1			3	1	1			6	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
chr12:86373821	p.R228Q	4
chr12:86374058	p.F73L	3
chr12:86377377	p.R149H	3
chr12:86373386	p.K326K	2
chr12:86373742	p.F254L	2
chr12:86373908	p.T321M	2
chr12:86373394	p.K305K	2
chr12:86374059	p.H162Q	2
chr12:86373396	p.R149C	2
chr12:86374139	p.R401W	2

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 MGAT4C 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 MGAT4C

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


AP3M1,BAG5,BEST3,METTL25,C1orf127,CCDC59,CDC42BPB, DAB1,ECD,ESPNP,FAM9A,KRR1,LRRIQ1,MARK3, MGAT4C,OR10J5,RCOR1,SEC24C,TMTC2,TSG1,ZNF839	ADAD1,LINC00293,CACNG2,CLEC17A,CR2,FCAMR,FCRL1, FCRL2,FCRL3,H1FOO,MGAT4C,MS4A1,NEUROG1,OR5B3, OR8G2,OR8I2,OR8K1,PAX5,PRNT,TEX11,ZNF679

ADCYAP1,ATP1B2,BAALC,BAI3,CPT1C,EPHA5,FAM43B, FOXD3,GPR162,GPR88,JAKMIP2,KCNT2,LDOC1,LRRC4C, MFAP4,MGAT4C,MLLT11,RGAG4,SLC26A10,TRO,ZNF385D	C1QTNF3,CADM2,CALY,CAV2,ELAVL4,FXYD1,GAP43, GNG3,GPM6B,MAB21L1,MGAT4C,MPZ,MYOT,NKX3-1, OLFM3,PLP1,PMP2,RASGEF1C,SRSF12,RNF217-AS1,TTYH1

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 MGAT4C

There's no related Drug.

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Cross referenced IDs for MGAT4C

* 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