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 LPGAT1

Basic gene info.	Gene symbol	LPGAT1
	Gene name	lysophosphatidylglycerol acyltransferase 1
	Synonyms	FAM34A\|FAM34A1\|NET8
	Cytomap	UCSC genome browser: 1q32
	Genomic location	chr1 :211916798-212004114
	Type of gene	protein-coding
	RefGenes	NM_014873.2,
	Ensembl id	ENSG00000123684
	Description	acyl-CoA:lysophosphatidylglycerol acyltransferase 1family with sequence similarity 34, member A
	Modification date	20141207
dbXrefs	MIM : 610473
	HGNC : HGNC
	Ensembl : ENSG00000123684
	HPRD : 14304
	Vega : OTTHUMG00000037120
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_LPGAT1
	BioGPS: 9926
	Gene Expression Atlas: ENSG00000123684
	The Human Protein Atlas: ENSG00000123684
Pathway	NCI Pathway Interaction Database: LPGAT1
	KEGG: LPGAT1
	REACTOME: LPGAT1
	ConsensusPathDB
	Pathway Commons: LPGAT1
Metabolism	MetaCyc: LPGAT1
	HUMANCyc: LPGAT1
Regulation	Ensembl's Regulation: ENSG00000123684
	miRBase: chr1 :211,916,798-212,004,114
	TargetScan: NM_014873
	cisRED: ENSG00000123684
Context	iHOP: LPGAT1
	cancer metabolism search in PubMed: LPGAT1
	UCL Cancer Institute: LPGAT1
Assigned class in ccmGDB	C

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Phenotypic Information for LPGAT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: LPGAT1
	Familial Cancer Database: LPGAT1

* 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_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: LPGAT1
	MedGen: LPGAT1 (Human Medical Genetics with Condition)
	ClinVar: LPGAT1
Phenotype	MGI: LPGAT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: LPGAT1

Mutations for LPGAT1

* 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	LPGAT1	chr1	211917130	211917130	LPGAT1	chr1	211934321	211934321
ovary	LPGAT1	chr1	211930742	211930762		chr1	211902349	211902369
ovary	LPGAT1	chr1	211973826	211973846	LPGAT1	chr1	211974009	211974029
ovary	LPGAT1	chr1	211981807	211981827		chr1	211879167	211879187
pancreas	LPGAT1	chr1	211943519	211943539		chr1	221720003	221720023
pancreas	LPGAT1	chr1	211986010	211986030	LPGAT1	chr1	211985608	211985628

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 LPGAT1 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
CB267058	LPGAT1	1	87	1	211950561	211950646	SIX1	83	263	14	61112817	61112995
BE936059	CAMK2N1	10	401	1	20808994	20809386	LPGAT1	401	574	1	211983165	211983484
AW948393	LPGAT1	8	125	1	211972542	211972658	PCSK7	122	195	11	117076940	117077012

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=24)	Stat. for Synonymous SNVs (# total SNVs=7)

Stat. for Deletions (# total SNVs=1)	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
chr1:211956632-211956632	p.L222L	4
chr1:211924401-211924401	p.P288L	2
chr1:211956832-211956832	p.R156C	2
chr1:211952357-211952357	p.I253L	1
chr1:211961026-211961026	p.Y134C	1
chr1:211923374-211923374	p.K327R	1
chr1:212002483-212002483	p.K52K	1
chr1:211952371-211952371	p.G248D	1
chr1:211961039-211961039	p.H130Y	1
chr1:211924348-211924348	p.R306W	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	1	4								2	3	1			5	1		5
# mutation	2	1	1	4								2	3	1			5	1		5
nonsynonymous SNV	1	1	1	2								2	2	1			2	1		5
synonymous SNV	1			2									1				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
chr1:211956832	p.R156C	2
chr1:211956806	p.R306W	1
chr1:212002626	p.L110L	1
chr1:211924401	p.P288L	1
chr1:211952301	p.K52K	1
chr1:211961026	p.I271I	1
chr1:211952327	p.Q44H	1
chr1:211961039	p.E263K	1
chr1:211952346	p.V40E	1
chr1:211966418	p.T256T	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 LPGAT1 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 LPGAT1

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


ANGEL2,BAGE2,SDE2,CCDC91,CD177,CD46,CEP350, EXOC8,FLVCR1,INTS7,LPGAT1,NSL1,OR10J1,IER3___SRGN, PSG11,PSG2,PSG7,RAB3GAP2,RPS6KC1,SLC22A10,TEX101	ANGPT1,ARHGAP21,ASPH,COBLL1,DDHD2,DYNC1LI2,ECM2, GNG2,IMPAD1,ITGA1,ITGB1,KLHL5,LPGAT1,NEK7, PALM2-AKAP2,PDZD2,PTPN11,RABL3,SEPT11,SORBS1,STS

ADIPOR1,ANGEL2,ARL8A,COPA,FAM20B,FBXO28,IRF6, KDM5B,CERS2,LPGAT1,NCSTN,NUCKS1,PPP2R5A,RPRD2, STX6,TP53BP2,TROVE2,UBE2Q1,WDR26,ZBTB41,ZC3H11A	ABCG8,CLDN2,DEFA5,DEFA6,DSG3,RMDN3,GALNT14, KHK,LPGAT1,LRAT,MTTP,NTS,PDZD7,REG3A, SEC14L2,SLC28A1,SLC2A5,SLC5A1,SLC6A20,TMEM229A,TNFSF15

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 LPGAT1

There's no related Drug.

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Cross referenced IDs for LPGAT1

* 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