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 LPCAT1

Basic gene info.	Gene symbol	LPCAT1
	Gene name	lysophosphatidylcholine acyltransferase 1
	Synonyms	AYTL2\|PFAAP3\|lpcat
	Cytomap	UCSC genome browser: 5p15.33
	Genomic location	chr5 :1461541-1524076
	Type of gene	protein-coding
	RefGenes	NM_024830.3,
	Ensembl id	ENSG00000153395
	Description	1-acylglycerophosphocholine O-acyltransferase1-alkylglycerophosphocholine O-acetyltransferaseLPC acyltransferase 1LPCAT-1acetyl-CoA:lyso-PAF acetyltransferaseacetyl-CoA:lyso-platelet-activating factor acetyltransferaseacyl-CoA:lysophosphatidylcholin
	Modification date	20141207
dbXrefs	MIM : 610472
	HGNC : HGNC
	Ensembl : ENSG00000153395
	HPRD : 08572
	Vega : OTTHUMG00000131017
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_LPCAT1
	BioGPS: 79888
	Gene Expression Atlas: ENSG00000153395
	The Human Protein Atlas: ENSG00000153395
Pathway	NCI Pathway Interaction Database: LPCAT1
	KEGG: LPCAT1
	REACTOME: LPCAT1
	ConsensusPathDB
	Pathway Commons: LPCAT1
Metabolism	MetaCyc: LPCAT1
	HUMANCyc: LPCAT1
Regulation	Ensembl's Regulation: ENSG00000153395
	miRBase: chr5 :1,461,541-1,524,076
	TargetScan: NM_024830
	cisRED: ENSG00000153395
Context	iHOP: LPCAT1
	cancer metabolism search in PubMed: LPCAT1
	UCL Cancer Institute: LPCAT1
Assigned class in ccmGDB	C

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Phenotypic Information for LPCAT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: LPCAT1
	Familial Cancer Database: LPCAT1

* 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: LPCAT1
	MedGen: LPCAT1 (Human Medical Genetics with Condition)
	ClinVar: LPCAT1
Phenotype	MGI: LPCAT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: LPCAT1

Mutations for LPCAT1

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LPCAT1 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
AV731790	LPCAT1	9	133	5	1465752	1465876	SYT1	134	585	12	79845330	79845786
AV729999	LPCAT1	6	129	5	1465749	1465876	SYT1	130	423	12	79845330	79845628
BG003119	TRIM25	14	238	17	54972334	54972559	LPCAT1	235	579	5	1476829	1477175
DB311369	LPCAT1	1	56	5	1461544	1461599	ENTPD7	52	317	10	101468342	101468607
BM693256	AP1S2	19	292	X	15845010	15845283	LPCAT1	283	449	5	1461785	1461951
AK123516	ENTPD7	1	1766	10	101466842	101468607	LPCAT1	1762	1817	5	1461544	1461599

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=47)	Stat. for Synonymous SNVs (# total SNVs=25)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=2)

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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
chr5:1494910-1494910	p.A133V	3
chr5:1501684-1501684	p.R57Q	3
chr5:1467001-1467001	p.Y428C	2
chr5:1463838-1463838	p.N511N	2
chr5:1494882-1494882	p.I142I	2
chr5:1474684-1474684	p.R339Q	2
chr5:1494891-1494891	p.F139F	2
chr5:1466919-1466919	p.T455T	2
chr5:1489959-1489959	p.I170V	2
chr5:1466983-1466983	p.G434D	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	2	1	9	1		2		1	1		11	3	4		1	9	6		11
# mutation	1	2	1	9	1		2		1	1		11	3	4		1	9	6		14
nonsynonymous SNV	1	2		5					1			9		3			4	5		6
synonymous SNV			1	4	1		2			1		2	3	1		1	5	1		8

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
chr5:1463838	p.N511N	2
chr5:1494882	p.R339R	2
chr5:1494891	p.R193Q	2
chr5:1489889	p.R177R	2
chr5:1489938	p.I142I	2
chr5:1474683	p.F139F	2
chr5:1488543	p.T210T	2
chr5:1466877	p.Q202E	1
chr5:1494858	p.L132L	1
chr5:1501585	p.D386A	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 LPCAT1 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 LPCAT1

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


BRD9,CCDC127,CCT5,CEP72,CLPTM1L,DAP,EXOC3, LOC25845,LPCAT1,MED10,MRPL36,MYBL2,NDUFS6,NSUN2, PAPD7,PDCD6,PDIA4,POLR2D,SDHA,SLC12A7,TRIP13	CALR,CKAP4,CNPY3,DNAJB11,GNA15,HM13,HSPA5, IGFBP4,LPCAT1,MANF,ORAI2,PDIA3,PDIA3P1,PDIA4, PDIA5,PDIA6,RGS19,RPN1,SEC61A1,TIMP1,TMED9

ADAM28,AGR2,C14orf184,CATSPERB,CDC42EP1,CHST6,CRELD2, CYB561,DUSP4,ELOVL3,FKBP11,FUT8,KCNK6,KDELR3, LPCAT1,LYN,LYSMD2,ODF3B,PFKP,RARRES1,VNN1	ATP10D,C1orf162,C1S,C2CD4A,CDH3,FAM167B,HAMP, IFI16,LILRA6,LPCAT1,NRROS,MAPK11,MYO3B,RAMP3, RILPL2,SLC43A3,SLFN11,ST3GAL5,TMEM106A,TNFAIP2,UPP2

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 LPCAT1

There's no related Drug.

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Cross referenced IDs for LPCAT1

* 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