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 LPCAT4
Basic gene info.Gene symbolLPCAT4
Gene namelysophosphatidylcholine acyltransferase 4
SynonymsAGPAT7|AYTL3|LPAAT-eta|LPEAT2
CytomapUCSC genome browser: 15q14
Genomic locationchr15 :34651088-34659395
Type of geneprotein-coding
RefGenesNM_153613.2,
Ensembl idENSG00000176454
Description1-AGP acyltransferase 71-AGPAT 71-acylglycerol-3-phosphate O-acyltransferase 7 (lysophosphatidic acid acyltransferase, eta)1-acylglycerophosphocholine O-acyltransferase1-acylglycerophosphoserine O-acyltransferase1-alkenylglycerophosphoethanolamine O-
Modification date20141207
dbXrefs MIM : 612039
HGNC : HGNC
Ensembl : ENSG00000176454
HPRD : 08315
Vega : OTTHUMG00000172349
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LPCAT4
BioGPS: 254531
Gene Expression Atlas: ENSG00000176454
The Human Protein Atlas: ENSG00000176454
PathwayNCI Pathway Interaction Database: LPCAT4
KEGG: LPCAT4
REACTOME: LPCAT4
ConsensusPathDB
Pathway Commons: LPCAT4
MetabolismMetaCyc: LPCAT4
HUMANCyc: LPCAT4
RegulationEnsembl's Regulation: ENSG00000176454
miRBase: chr15 :34,651,088-34,659,395
TargetScan: NM_153613
cisRED: ENSG00000176454
ContextiHOP: LPCAT4
cancer metabolism search in PubMed: LPCAT4
UCL Cancer Institute: LPCAT4
Assigned class in ccmGDBC

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Phenotypic Information for LPCAT4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LPCAT4
Familial Cancer Database: LPCAT4
* 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: LPCAT4
MedGen: LPCAT4 (Human Medical Genetics with Condition)
ClinVar: LPCAT4
PhenotypeMGI: LPCAT4 (International Mouse Phenotyping Consortium)
PhenomicDB: LPCAT4

Mutations for LPCAT4
* 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 LPCAT4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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          
GAIN (# sample)                 
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=27)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr15:34654982-34654982p.?3
chr15:34652411-34652411p.?2
chr15:34656262-34656262p.P202S2
chr15:34653621-34653621p.A375T2
chr15:34654440-34654440p.E323Q1
chr15:34657824-34657824p.A65T1
chr15:34655878-34655878p.R232H1
chr15:34651395-34651395p.S503L1
chr15:34652368-34652368p.L396V1
chr15:34656516-34656516p.?1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   51   1  51   93 3
# mutation   51   1  51   103 4
nonsynonymous SNV   4    1  3    63 3
synonymous SNV   11      21   4  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
chr15:34656452p.P202H1
chr15:34651440p.R488L1
chr15:34653713p.P202S1
chr15:34656463p.R488C1
chr15:34651441p.P196P1
chr15:34654491p.G463D1
chr15:34657242p.T190T1
chr15:34651801p.S443L1
chr15:34655878p.R188L1
chr15:34657245p.E422D1

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 LPCAT4 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 LPCAT4

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

ACD,AGAP3,CSK,CYBA,E2F4,EFHD2,FADS3,
LPCAT4,LYSMD2,MIIP,NOP10,RHOG,RIN1,RNF166,
RPS6KA4,SH3BGRL3,SH3BP1,TAZ,EMC4,TNFRSF25,ZNF276
ADM5,CALHM2,CLDN15,CYP21A2,ACKR1,FAM167B,TMEM255B,
FLT3LG,FXYD5,IFI27L2,IFITM2,IFITM3,LPCAT4,LYL1,
MFNG,RASIP1,RHOG,SECTM1,SPNS2,TMEM173,TMEM39B

AGR2,BARX2,GDPGP1,TMEM246,CAPN5,RHOV___CHP1,CIB1,
CREB3L1,CYB5D2,ABHD17C,INPP1,KCNK1,LIPH,LPCAT4,
MARVELD3,PLLP,REG4,SCAMP2,SLC17A5,TSPAN3,VWA3B
AP1G2,ARHGEF10L,PROSER2,C10orf95,TMEM246,C9orf152,SPECC1,
ESRP2,FLJ32063,FOXD2,FUK,GOLM1,HOXB9,ILDR1,
LIMK2,LPAR5,LPCAT4,PPFIA3,PWWP2B,TMEM44,ZBTB7C
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 LPCAT4


There's no related Drug.
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Cross referenced IDs for LPCAT4
* 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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