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 LPGAT1
Basic gene info.Gene symbolLPGAT1
Gene namelysophosphatidylglycerol acyltransferase 1
SynonymsFAM34A|FAM34A1|NET8
CytomapUCSC genome browser: 1q32
Genomic locationchr1 :211916798-212004114
Type of geneprotein-coding
RefGenesNM_014873.2,
Ensembl idENSG00000123684
Descriptionacyl-CoA:lysophosphatidylglycerol acyltransferase 1family with sequence similarity 34, member A
Modification date20141207
dbXrefs MIM : 610473
HGNC : HGNC
Ensembl : ENSG00000123684
HPRD : 14304
Vega : OTTHUMG00000037120
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LPGAT1
BioGPS: 9926
Gene Expression Atlas: ENSG00000123684
The Human Protein Atlas: ENSG00000123684
PathwayNCI Pathway Interaction Database: LPGAT1
KEGG: LPGAT1
REACTOME: LPGAT1
ConsensusPathDB
Pathway Commons: LPGAT1
MetabolismMetaCyc: LPGAT1
HUMANCyc: LPGAT1
RegulationEnsembl's Regulation: ENSG00000123684
miRBase: chr1 :211,916,798-212,004,114
TargetScan: NM_014873
cisRED: ENSG00000123684
ContextiHOP: LPGAT1
cancer metabolism search in PubMed: LPGAT1
UCL Cancer Institute: LPGAT1
Assigned class in ccmGDBC

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Phenotypic Information for LPGAT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LPGAT1
Familial Cancer Database: LPGAT1
* 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: LPGAT1
MedGen: LPGAT1 (Human Medical Genetics with Condition)
ClinVar: LPGAT1
PhenotypeMGI: LPGAT1 (International Mouse Phenotyping Consortium)
PhenomicDB: LPGAT1

Mutations for LPGAT1
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastLPGAT1chr1211917130211917130LPGAT1chr1211934321211934321
ovaryLPGAT1chr1211930742211930762chr1211902349211902369
ovaryLPGAT1chr1211973826211973846LPGAT1chr1211974009211974029
ovaryLPGAT1chr1211981807211981827chr1211879167211879187
pancreasLPGAT1chr1211943519211943539chr1221720003221720023
pancreasLPGAT1chr1211986010211986030LPGAT1chr1211985608211985628
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LPGAT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CB267058LPGAT11871211950561211950646SIX183263146111281761112995
BE936059CAMK2N11040112080899420809386LPGAT14015741211983165211983484
AW948393LPGAT181251211972542211972658PCSK712219511117076940117077012

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        
GAIN (# sample)      1 1        
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr1:211956632-211956632p.L222L4
chr1:211924401-211924401p.P288L2
chr1:211956832-211956832p.R156C2
chr1:211961039-211961039p.H130Y1
chr1:211924348-211924348p.R306W1
chr1:212002500-212002500p.R47*1
chr1:211956599-211956600p.S233fs*111
chr1:211966416-211966416p.L119M1
chr1:211924387-211924387p.P293T1
chr1:212002520-212002520p.V40E1

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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
# sample2114       231  51 5
# mutation2114       231  51 5
nonsynonymous SNV1112       221  21 5
synonymous SNV1  2        1   3   
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
chr1:211956832p.R156C2
chr1:211952301p.E263K1
chr1:211961026p.V40E1
chr1:211952327p.T256T1
chr1:211961039p.V31F1
chr1:211952346p.T256M1
chr1:211966418p.N29S1
chr1:211952347p.I253L1
chr1:211966441p.L5L1
chr1:211952357p.G248D1

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 LPGAT1 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 LPGAT1

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

ANGEL2,BAGE2,SDE2,CCDC91,CD177,CD46,CEP350,
EXOC8,FLVCR1,INTS7,LPGAT1,NSL1,OR10J1,IER3___SRGN,
PSG11,PSG2,PSG7,RAB3GAP2,RPS6KC1,SLC22A10,TEX101
ANGPT1,ARHGAP21,ASPH,COBLL1,DDHD2,DYNC1LI2,ECM2,
GNG2,IMPAD1,ITGA1,ITGB1,KLHL5,LPGAT1,NEK7,
PALM2-AKAP2,PDZD2,PTPN11,RABL3,SEPT11,SORBS1,STS

ADIPOR1,ANGEL2,ARL8A,COPA,FAM20B,FBXO28,IRF6,
KDM5B,CERS2,LPGAT1,NCSTN,NUCKS1,PPP2R5A,RPRD2,
STX6,TP53BP2,TROVE2,UBE2Q1,WDR26,ZBTB41,ZC3H11A
ABCG8,CLDN2,DEFA5,DEFA6,DSG3,RMDN3,GALNT14,
KHK,LPGAT1,LRAT,MTTP,NTS,PDZD7,REG3A,
SEC14L2,SLC28A1,SLC2A5,SLC5A1,SLC6A20,TMEM229A,TNFSF15
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 LPGAT1


There's no related Drug.
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Cross referenced IDs for LPGAT1
* 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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