Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolLPCAT1
Gene namelysophosphatidylcholine acyltransferase 1
SynonymsAYTL2|PFAAP3|lpcat
CytomapUCSC genome browser: 5p15.33
Genomic locationchr5 :1461541-1524076
Type of geneprotein-coding
RefGenesNM_024830.3,
Ensembl idENSG00000153395
Description1-acylglycerophosphocholine O-acyltransferase1-alkylglycerophosphocholine O-acetyltransferaseLPC acyltransferase 1LPCAT-1acetyl-CoA:lyso-PAF acetyltransferaseacetyl-CoA:lyso-platelet-activating factor acetyltransferaseacyl-CoA:lysophosphatidylcholin
Modification date20141207
dbXrefs MIM : 610472
HGNC : HGNC
Ensembl : ENSG00000153395
HPRD : 08572
Vega : OTTHUMG00000131017
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LPCAT1
BioGPS: 79888
Gene Expression Atlas: ENSG00000153395
The Human Protein Atlas: ENSG00000153395
PathwayNCI Pathway Interaction Database: LPCAT1
KEGG: LPCAT1
REACTOME: LPCAT1
ConsensusPathDB
Pathway Commons: LPCAT1
MetabolismMetaCyc: LPCAT1
HUMANCyc: LPCAT1
RegulationEnsembl's Regulation: ENSG00000153395
miRBase: chr5 :1,461,541-1,524,076
TargetScan: NM_024830
cisRED: ENSG00000153395
ContextiHOP: LPCAT1
cancer metabolism search in PubMed: LPCAT1
UCL Cancer Institute: LPCAT1
Assigned class in ccmGDBC

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Phenotypic Information for LPCAT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: LPCAT1
MedGen: LPCAT1 (Human Medical Genetics with Condition)
ClinVar: LPCAT1
PhenotypeMGI: LPCAT1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LPCAT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AV731790LPCAT19133514657521465876SYT1134585127984533079845786
AV729999LPCAT16129514657491465876SYT1130423127984533079845628
BG003119TRIM2514238175497233454972559LPCAT1235579514768291477175
DB311369LPCAT1156514615441461599ENTPD75231710101468342101468607
BM693256AP1S219292X1584501015845283LPCAT1283449514617851461951
AK123516ENTPD71176610101466842101468607LPCAT117621817514615441461599

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample   1    1 1  1 1 
GAIN (# sample)   1    1 1  1   
LOSS (# sample)               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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr5:1494910-1494910p.A133V3
chr5:1501684-1501684p.R57Q3
chr5:1467001-1467001p.Y428C2
chr5:1463838-1463838p.N511N2
chr5:1494882-1494882p.I142I2
chr5:1474684-1474684p.R339Q2
chr5:1494891-1494891p.F139F2
chr5:1466919-1466919p.T455T2
chr5:1489959-1489959p.I170V2
chr5:1466983-1466983p.G434D2

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample12191 2 11 1134 196 11
# mutation12191 2 11 1134 196 14
nonsynonymous SNV12 5    1  9 3  45 6
synonymous SNV  141 2  1 231 151 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr5:1463838p.N511N2
chr5:1494882p.R339R2
chr5:1494891p.R193Q2
chr5:1489889p.R177R2
chr5:1489938p.I142I2
chr5:1474683p.F139F2
chr5:1488543p.T210T2
chr5:1474752p.F513F1
chr5:1495000p.M387I1
chr5:1463832p.T210I1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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



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