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 LPCAT2
Basic gene info.Gene symbolLPCAT2
Gene namelysophosphatidylcholine acyltransferase 2
SynonymsAYTL1|LysoPAFAT
CytomapUCSC genome browser: 16q12.2
Genomic locationchr16 :55542912-55620582
Type of geneprotein-coding
RefGenesNM_017839.4,
Ensembl idENSG00000087253
Description1-AGP acyltransferase 111-AGPAT 111-acylglycerol-3-phosphate O-acyltransferase 111-acylglycerophosphocholine O-acyltransferase1-alkylglycerophosphocholine O-acetyltransferaseLPAAT-alphaLPC acyltransferase 2LPCAT-2acetyl-CoA:lyso-PAF acetyltransfer
Modification date20141207
dbXrefs MIM : 612040
HGNC : HGNC
Ensembl : ENSG00000087253
HPRD : 07913
Vega : OTTHUMG00000133238
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LPCAT2
BioGPS: 54947
Gene Expression Atlas: ENSG00000087253
The Human Protein Atlas: ENSG00000087253
PathwayNCI Pathway Interaction Database: LPCAT2
KEGG: LPCAT2
REACTOME: LPCAT2
ConsensusPathDB
Pathway Commons: LPCAT2
MetabolismMetaCyc: LPCAT2
HUMANCyc: LPCAT2
RegulationEnsembl's Regulation: ENSG00000087253
miRBase: chr16 :55,542,912-55,620,582
TargetScan: NM_017839
cisRED: ENSG00000087253
ContextiHOP: LPCAT2
cancer metabolism search in PubMed: LPCAT2
UCL Cancer Institute: LPCAT2
Assigned class in ccmGDBC

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Phenotypic Information for LPCAT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LPCAT2
Familial Cancer Database: LPCAT2
* 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: LPCAT2
MedGen: LPCAT2 (Human Medical Genetics with Condition)
ClinVar: LPCAT2
PhenotypeMGI: LPCAT2 (International Mouse Phenotyping Consortium)
PhenomicDB: LPCAT2

Mutations for LPCAT2
* 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 LPCAT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AJ420584LPCAT2251589165556582455617581TXNDC515841900680142148014530
AI333351ATP6V1D3350146780458967804936LPCAT2348462165560070055600814
AA602968LPCAT28107165562002855620127LPCAT2103429165561970655620032
CN286009LPCAT21374165561872255618783LPCAT255426165561873455619115

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 # sample1    1    2  1   
GAIN (# sample)             1   
LOSS (# sample)1    1    2      
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=32)
Stat. for Synonymous SNVs
(# total SNVs=10)
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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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
chr16:55579721-55579721p.L309L3
chr16:55613030-55613030p.V442I2
chr16:55613052-55613052p.T449M2
chr16:55585003-55585003p.L402F2
chr16:55568366-55568366p.T258T2
chr16:55616885-55616885p.L504L1
chr16:55579714-55579714p.R307Q1
chr16:55584910-55584910p.A371S1
chr16:55559500-55559500p.A84A1
chr16:55608625-55608625p.I433T1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   61 2 1  73   79 6
# mutation   61 2 1  73   710 7
nonsynonymous SNV   41 2 1  43   38 6
synonymous SNV   2       3    42 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
chr16:55613052p.T449M2
chr16:55584911p.A371V2
chr16:55583308p.A311T1
chr16:55613023p.L439L1
chr16:55559537p.H97Y1
chr16:55565881p.C326C1
chr16:55583314p.V442I1
chr16:55613030p.L114M1
chr16:55562317p.G333R1
chr16:55566747p.S121P1

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 LPCAT2 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 LPCAT2

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

ARHGAP31,BICC1,EOGT,CARD6,DPYD,DSE,DST,
FAM126A,KCTD12,LHFPL2,LPCAT2,LRCH1,LUZP1,PKD2,
PLSCR4,PROS1,QKI,RBMS1,RCBTB2,SOCS5,TSHZ2
TMEM237,TDRP,COMMD2,DENND6A,FAM13B,ZC2HC1A,CCSER1,
FEM1B,IL1RAP,LPCAT2,LZTFL1,MCTP2,NAP1L2,NUDT21,
PRKCI,RBMXL1,SMEK1,TP63,USP31,ZNF10,ZNF136

RGCC,C15orf26,CSRNP3,DERL1,DPY19L4,EBAG9,FAM91A1,
HPCAL1,UFL1,LPCAT2,MAL2,MBNL2,NEBL,OXR1,
PCSK1,PLEKHB1,PTK2,RAB2A,TMEM67,VEZF1,ZBTB10
ASUN,TMA16,C4orf46,CLINT1,GPX2,GSTCD,LPCAT2,
MRPS27,MTHFD2,PGA4,PM20D2,PPAT,PRPS2,RCN1,
RNF183,SKP2,SLC10A7,SORD,TMEM173,WDR75,ZWILCH
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 LPCAT2


There's no related Drug.
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Cross referenced IDs for LPCAT2
* 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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