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 AGPAT5
Basic gene info.Gene symbolAGPAT5
Gene name1-acylglycerol-3-phosphate O-acyltransferase 5
Synonyms1AGPAT5|LPAATE
CytomapUCSC genome browser: 8p23.1
Genomic locationchr8 :6565877-6619021
Type of geneprotein-coding
RefGenesNM_018361.3,
Ensembl idENSG00000155189
Description1-AGP acyltransferase 51-AGPAT 51-acyl-sn-glycerol-3-phosphate acyltransferase epsilon1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)lysophosphatidic acid acyltransferase epsilon
Modification date20141207
dbXrefs MIM : 614796
HGNC : HGNC
HPRD : 12438
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AGPAT5
BioGPS: 55326
Gene Expression Atlas: ENSG00000155189
The Human Protein Atlas: ENSG00000155189
PathwayNCI Pathway Interaction Database: AGPAT5
KEGG: AGPAT5
REACTOME: AGPAT5
ConsensusPathDB
Pathway Commons: AGPAT5
MetabolismMetaCyc: AGPAT5
HUMANCyc: AGPAT5
RegulationEnsembl's Regulation: ENSG00000155189
miRBase: chr8 :6,565,877-6,619,021
TargetScan: NM_018361
cisRED: ENSG00000155189
ContextiHOP: AGPAT5
cancer metabolism search in PubMed: AGPAT5
UCL Cancer Institute: AGPAT5
Assigned class in ccmGDBC

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Phenotypic Information for AGPAT5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AGPAT5
Familial Cancer Database: AGPAT5
* 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
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: AGPAT5
MedGen: AGPAT5 (Human Medical Genetics with Condition)
ClinVar: AGPAT5
PhenotypeMGI: AGPAT5 (International Mouse Phenotyping Consortium)
PhenomicDB: AGPAT5

Mutations for AGPAT5
* 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
pancreasAGPAT5chr865863286586328chr81292127012921270
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 AGPAT5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA830108AGPAT51266866143836614648AGPAT5264694866126996613122
BE089963AGPAT515154866164876616626HNRNPH3152431107010256270102841

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)                 
LOSS (# sample)      1 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=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=12)
Stat. for Deletions
(# total SNVs=2)
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
chr8:6612681-6612681p.F285F5
chr8:6588252-6588252p.I104V2
chr8:6605274-6605274p.A224S2
chr8:6566351-6566351p.L54L2
chr8:6590133-6590133p.R153*2
chr8:6599221-6599221p.P179S2
chr8:6612576-6612576p.F250F1
chr8:6614771-6614771p.K319K1
chr8:6582429-6582429p.N86K1
chr8:6599260-6599260p.A192T1

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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   8  1 31 11   32 8
# mutation   8  1 31 11   32 9
nonsynonymous SNV   3    31 11   22 6
synonymous SNV   5  1         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
chr8:6612681p.F285F2
chr8:6614774p.I287V1
chr8:6588236p.D98D1
chr8:6612607p.F295L1
chr8:6614805p.L128F1
chr8:6588326p.D300E1
chr8:6612617p.A134V1
chr8:6614840p.P301L1
chr8:6588343p.P179S1
chr8:6612621p.K319K1

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 AGPAT5 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 AGPAT5

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

AGPAT5,CNOT7,ERI1,ERICH1,FZD3,HEATR1,INTS10,
KCTD9,LONRF1,MCPH1,MFHAS1,MTMR9,PM20D2,PPP2R2A,
RPL23AP53,SEH1L,SLC39A14,TNKS,VPS37A,WRN,XPO7
AGPAT5,DCAF12,EPT1,FZD3,GNPNAT1,GPD2,MARS2,
MRPL42,NAALADL2,NKRF,PAICS,PIGN,PPAT,PRKCI,
RPAP3,SRPK1,SSX2IP,SUV39H2,TDG,TMEM33,USP10

AGPAT5,CCDC25,CNOT7,DCTN6,ELP3,ERI1,ESCO2,
FBXO25,FDFT1,FUT10,FZD3,GSR,GTF2E2,INTS10,
MAK16,MCPH1,PBK,PINX1,PPP2R2A,UBXN8,VPS37A
AGPAT5,FAM210A,DARS2,HSPA9,KCNN4,LRPPRC,MARS2,
MCCC2,MECOM,MGST1,MIPEP,MRPS30,PIGU,PPIF,
PPIP5K2,PTDSS1,RPIA,SEH1L,SRPK1,STARD7,WARS2
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 AGPAT5


There's no related Drug.
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Cross referenced IDs for AGPAT5
* 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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