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 AGPAT6

Basic gene info.	Gene symbol	AGPAT6
	Gene name	1-acylglycerol-3-phosphate O-acyltransferase 6
	Synonyms	1-AGPAT 6\|LPAAT-zeta\|LPAATZ\|TSARG7
	Cytomap	UCSC genome browser: 8p11.21
	Genomic location	chr8 :41435706-41482520
	Type of gene	protein-coding
	RefGenes	NM_178819.3,
	Ensembl id	ENSG00000158669
	Description	1-AGP acyltransferase 61-acyl-sn-glycerol-3-phosphate acyltransferase zeta1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)glycerol-3-phosphate acyltransferase 6lysophosphatidic acid acyltransferase zetatest
	Modification date	20141207
dbXrefs	MIM : 608143
	HGNC : HGNC
	Ensembl : ENSG00000158669
	HPRD : 12175
	Vega : OTTHUMG00000164082
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_AGPAT6
	BioGPS: 137964
	Gene Expression Atlas: ENSG00000158669
	The Human Protein Atlas: ENSG00000158669
Pathway	NCI Pathway Interaction Database: AGPAT6
	KEGG: AGPAT6
	REACTOME: AGPAT6
	ConsensusPathDB
	Pathway Commons: AGPAT6
Metabolism	MetaCyc: AGPAT6
	HUMANCyc: AGPAT6
Regulation	Ensembl's Regulation: ENSG00000158669
	miRBase: chr8 :41,435,706-41,482,520
	TargetScan: NM_178819
	cisRED: ENSG00000158669
Context	iHOP: AGPAT6
	cancer metabolism search in PubMed: AGPAT6
	UCL Cancer Institute: AGPAT6
Assigned class in ccmGDB	C

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Phenotypic Information for AGPAT6(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: AGPAT6
	Familial Cancer Database: AGPAT6

* 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
KEGG_GLYCEROLIPID_METABOLISM KEGG_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: AGPAT6
	MedGen: AGPAT6 (Human Medical Genetics with Condition)
	ClinVar: AGPAT6
Phenotype	MGI: AGPAT6 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: AGPAT6

Mutations for AGPAT6

* 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
breast	AGPAT6	chr8	41457837	41457837	AGPAT6	chr8	41469318	41469318
pancreas	AGPAT6	chr8	41443769	41443789	AGPAT6	chr8	41449400	41449420

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 AGPAT6 related fusion information.

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

AW264211

CDK2AP2

113

67273972

67274068

AGPAT6

109

597

41469732

41476461

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			5		3		1				1		1
GAIN (# sample)	5			3			5		2		1				1		1
LOSS (# sample)	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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=29)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr8:41456786-41456786	p.R43H	4
chr8:41469477-41469477	p.R223*	3
chr8:41467367-41467367	p.W143*	2
chr8:41469749-41469749	p.P251L	2
chr8:41467379-41467379	p.S147S	2
chr8:41456817-41456817	p.I53M	2
chr8:41469728-41469728	p.C244S	1
chr8:41456755-41456755	p.P33S	1
chr8:41476277-41476277	p.M376I	1
chr8:41476308-41476308	p.Y387H	1

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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=2

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		2	1	7	1				3	1		4	1	1			2	4		6
# mutation		2	1	7	1				3	1		4	1	1			2	4		8
nonsynonymous SNV		2	1	4	1				3			2	1	1			2	2		5
synonymous SNV				3						1		2						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
chr8:41456786	p.S147S	2
chr8:41467379	p.R43H	2
chr8:41470394	p.G99C	1
chr8:41467422	p.G267C	1
chr8:41470463	p.D105E	1
chr8:41466955	p.V276L	1
chr8:41467449	p.F110F	1
chr8:41471927	p.H299Y	1
chr8:41467214	p.K312E	1
chr8:41468294	p.F116F	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 AGPAT6 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 AGPAT6

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


AGPAT6,AP3M2,ASH2L,BAG4,BRF2,SMIM19,DDHD2, FNTA,GINS4,GOLGA7,HGSNAT,IKBKB,KAT6A,POLB, PTH,RAB11FIP1,RNF170,SLC20A2,THAP1,VDAC3,WHSC1L1	ACBD6,AGPAT6,ALKBH2,CCT3,DDX54,EBNA1BP2,EIF3B, EXOSC5,MRTO4,NCL,NOP16,PES1,RRP1,RUVBL2, SHMT2,SMARCA4,SMARCD2,SND1,SURF6,TOP1MT,WDR74

AGPAT6,ANK1,FAM84B,FNTA,GINS4,GLYATL2,GOLGA7, HGSNAT,HOOK3,IKBKB,IMPAD1,KIAA1429,KAT6A,OR13C4, RB1CC1,RNF170,SLC20A2,SLC5A8,STXBP5L,TGS1,UBXN2B	AGPAT6,CCDC9,GTF3C1,HIPK2,HTT,IGF2R,KDM2A, MAVS,MYH9,MYO18A,PTPN23,RNF40,RRBP1,SAFB, SLC38A1,SMARCA4,UBAP2,UBN1,UPF1,USP7,VPS53

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 AGPAT6

There's no related Drug.

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Cross referenced IDs for AGPAT6

* 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