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 AGPAT3

Basic gene info.	Gene symbol	AGPAT3
	Gene name	1-acylglycerol-3-phosphate O-acyltransferase 3
	Synonyms	LPAAT-GAMMA1\|LPAAT3
	Cytomap	UCSC genome browser: 21q22.3
	Genomic location	chr21 :45345278-45407475
	Type of gene	protein-coding
	RefGenes	NM_001037553.1, NM_020132.4,
	Ensembl id	ENSG00000160216
	Description	1-AGP acyltransferase 31-AGPAT 31-acyl-sn-glycerol-3-phosphate acyltransferase gammalysophosphatidic acid acyltransferase gammalysophosphatidic acid acyltransferase-gamma1
	Modification date	20141207
dbXrefs	MIM : 614794
	HGNC : HGNC
	Ensembl : ENSG00000160216
	HPRD : 10637
	Vega : OTTHUMG00000086892
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_AGPAT3
	BioGPS: 56894
	Gene Expression Atlas: ENSG00000160216
	The Human Protein Atlas: ENSG00000160216
Pathway	NCI Pathway Interaction Database: AGPAT3
	KEGG: AGPAT3
	REACTOME: AGPAT3
	ConsensusPathDB
	Pathway Commons: AGPAT3
Metabolism	MetaCyc: AGPAT3
	HUMANCyc: AGPAT3
Regulation	Ensembl's Regulation: ENSG00000160216
	miRBase: chr21 :45,345,278-45,407,475
	TargetScan: NM_001037553
	cisRED: ENSG00000160216
Context	iHOP: AGPAT3
	cancer metabolism search in PubMed: AGPAT3
	UCL Cancer Institute: AGPAT3
Assigned class in ccmGDB	C

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Phenotypic Information for AGPAT3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: AGPAT3
	Familial Cancer Database: AGPAT3

* 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: AGPAT3
	MedGen: AGPAT3 (Human Medical Genetics with Condition)
	ClinVar: AGPAT3
Phenotype	MGI: AGPAT3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: AGPAT3

Mutations for AGPAT3

* 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	AGPAT3	chr21	45376064	45376084	AGPAT3	chr21	45384107	45384127
pancreas	AGPAT3	chr21	45348999	45349019	RUNX1	chr21	36167152	36167172

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 AGPAT3 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
BF955600	TMOD1	2	79	9	100353599	100353676	AGPAT3	75	141	21	45302061	45302127
AK125812	AGPAT3	1	78	21	45366864	45366941	ATP1A4	76	3797	1	160136317	160156576
DB062417	AGPAT3	1	78	21	45366864	45366941	ATP1A4	76	538	1	160136317	160137220
BF955597	TMOD1	1	90	9	100353587	100353676	AGPAT3	86	152	21	45302061	45302127

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

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=25)	Stat. for Synonymous SNVs (# total SNVs=12)

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
chr21:45402199-45402199	p.R353C	5
chr21:45379734-45379734	p.W58R	2
chr21:45379739-45379739	p.S59S	2
chr21:45379596-45379596	p.V12M	2
chr21:45401010-45401010	p.G328G	2
chr21:45390643-45390643	p.R207Q	1
chr21:45400872-45400872	p.D282D	1
chr21:45389131-45389131	p.R161C	1
chr21:45402243-45402243	p.Y367Y	1
chr21:45391304-45391304	p.G234R	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=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	2	2		8			1					2	2	1	1	1	6	3		5
# mutation	2	2		8			1					2	2	1	1	1	7	3		6
nonsynonymous SNV	2	2		4			1					2	1	1	1	1	6	2		4
synonymous SNV				4									1				1	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
chr21:45402199	p.R353C,AGPAT3	3
chr21:45387862	p.G328G,AGPAT3	2
chr21:45401010	p.E72Q,AGPAT3	2
chr21:45400968	p.T154N,AGPAT3	1
chr21:45387860	p.P295S,AGPAT3	1
chr21:45391304	p.R161H,AGPAT3	1
chr21:45400973	p.W314C,AGPAT3	1
chr21:45391317	p.R161R,AGPAT3	1
chr21:45400990	p.T316N,AGPAT3	1
chr21:45389009	p.T178M,AGPAT3	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 AGPAT3 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 AGPAT3

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


AGPAT3,BRWD1,DOPEY2,DSCR3,DYRK1A,HLCS,LSS, NDUFV3,PCNT,PFKL,PWP2,RRP1B,SLC19A1,SLC37A1, SUMO3,TRAPPC10,TTC3,UBE2G2,URB1,WRB,ZBTB7B	ABCB6,AGPAT3,AIFM1,ALDH4A1,GUCD1,CRAT,CUX1, DKFZp779M0652,FITM2,GPI,HECTD3,ICMT,IGF2R,ITFG3, NPLOC4,PREB,PSMD2,SUOX,TRIM16L,VCP,ZFAND3

AGPAT3,C2CD2,CGN,DIP2A,DSCR3,DYRK1A,HLCS, LSS,MCM3AP,MYO18A,PCNT,PDXK,PFKL,PITPNM1, HELZ2,PWP2,RIPK4,RRP1B,TRAPPC10,UBE2G2,URB1	AGPAT3,ATG9A,C1orf115,ESPN,GDPD2,GNA11,HECA, HECTD3,KIAA0247,KIF3B,LASP1,LOC151534,MAST2,MYO7B, PDXK,PIGS,POR,RXRA,SLC9A3R1,SPINT1,TGOLN2

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 AGPAT3

There's no related Drug.

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Cross referenced IDs for AGPAT3

* 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