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 LPCAT3
Basic gene info.Gene symbolLPCAT3
Gene namelysophosphatidylcholine acyltransferase 3
SynonymsC3F|LPCAT|LPLAT 5|LPSAT|MBOAT5|OACT5|nessy
CytomapUCSC genome browser: 12p13
Genomic locationchr12 :7085346-7125842
Type of geneprotein-coding
RefGenesNM_005768.5,
Ensembl idENSG00000268829
Description1-acylglycerophosphocholine O-acyltransferase1-acylglycerophosphoserine O-acyltransferaseO-acyltransferase (membrane bound) domain containing 5O-acyltransferase domain-containing protein 5lyso-PC acyltransferase 3lyso-PS acyltransferaselysophosphati
Modification date20141207
dbXrefs MIM : 611950
HGNC : HGNC
Ensembl : ENSG00000111684
HPRD : 12816
Vega : OTTHUMG00000168970
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LPCAT3
BioGPS: 10162
Gene Expression Atlas: ENSG00000268829
The Human Protein Atlas: ENSG00000268829
PathwayNCI Pathway Interaction Database: LPCAT3
KEGG: LPCAT3
REACTOME: LPCAT3
ConsensusPathDB
Pathway Commons: LPCAT3
MetabolismMetaCyc: LPCAT3
HUMANCyc: LPCAT3
RegulationEnsembl's Regulation: ENSG00000268829
miRBase: chr12 :7,085,346-7,125,842
TargetScan: NM_005768
cisRED: ENSG00000268829
ContextiHOP: LPCAT3
cancer metabolism search in PubMed: LPCAT3
UCL Cancer Institute: LPCAT3
Assigned class in ccmGDBC

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Phenotypic Information for LPCAT3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LPCAT3
Familial Cancer Database: LPCAT3
* 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: LPCAT3
MedGen: LPCAT3 (Human Medical Genetics with Condition)
ClinVar: LPCAT3
PhenotypeMGI: LPCAT3 (International Mouse Phenotyping Consortium)
PhenomicDB: LPCAT3

Mutations for LPCAT3
* 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 LPCAT3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI870471LPCAT355911271257487126194GSG1L81125162807474628304597

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 # sample21               
GAIN (# sample)21               
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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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=36)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted snv.

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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
chr12:7087511-7087511p.W344*3
chr12:7088678-7088678p.L247L2
chr12:7087528-7087528p.I339V2
chr12:7090313-7090313p.A177V2
chr12:7087832-7087832p.R269P2
chr12:7092611-7092611p.I81V1
chr12:7087516-7087516p.A343T1
chr12:7090783-7090783p.V157V1
chr12:7092663-7092663p.F63L1
chr12:7090169-7090169p.N225S1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 1  113  222   3 7
# mutation 1 1  113  232   3 7
nonsynonymous SNV 1 1   12  132   3 7
synonymous SNV      1 1  1        
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
chr12:7087581p.V294L1
chr12:7090771p.G293E1
chr12:7087608p.E292D1
chr12:7090783p.W288C1
chr12:7087663p.R233C1
chr12:7091052p.N225S1
chr12:7087665p.D218Y1
chr12:7091877p.F461I1
chr12:7086391p.G214E1
chr12:7087667p.M436T1

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 LPCAT3 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 LPCAT3

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

ACSM1,ALOX15B,C15orf43,APMAP,CD9,CHRNA2,COPS7A,
ISX,LPCAT3,LST-3TM12,M6PR,MPV17L,PNLIPRP3,SCP2,
SERHL2,SLCO1B1,SPINK8,SRD5A1,SULT1C3,TMEM62,UGT2B28
ABCC11,AFMID,AKR1A1,ALDH3B2,ALOX15B,GGT1,GGTLC2,
HMGCS2,HRASLS2,KYNU,CERS4,LPCAT3,MPV17L,MVK,
NSUN2,REEP6,SERHL2,SERHL,SPINK8,TMEM62,TMEM63C

ACADS,ARF3,RITA1,CA13,COPS7A,DGAT1,LPCAT3,
METTL7B,MLF2,OPLAH,PEBP1,PEX5,PLEKHG6,PRR13,
SLC7A9,SPAM1,SPPL3,SPSB2,TMBIM6,USP5,ZNF384
ACOX1,ANKS4B,ANO10,AP1AR,CEBPA,RHOV___CHP1,DOLPP1,
ESPN,GAREM,FAM73B,GNG12,HADHA,KALRN,LPCAT3,
MARVELD3,MGAT4A,MOGAT3,SEPHS2,SLC27A4,SLC41A2,SPHK2
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 LPCAT3


There's no related Drug.
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Cross referenced IDs for LPCAT3
* 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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