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 AGPAT6
Basic gene info.Gene symbolAGPAT6
Gene name1-acylglycerol-3-phosphate O-acyltransferase 6
Synonyms1-AGPAT 6|LPAAT-zeta|LPAATZ|TSARG7
CytomapUCSC genome browser: 8p11.21
Genomic locationchr8 :41435706-41482520
Type of geneprotein-coding
RefGenesNM_178819.3,
Ensembl idENSG00000158669
Description1-AGP acyltransferase 61-acyl-sn-glycerol-3-phosphate acyltransferase zeta1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)glycerol-3-phosphate acyltransferase 6lysophosphatidic acid acyltransferase zetatest
Modification date20141207
dbXrefs MIM : 608143
HGNC : HGNC
Ensembl : ENSG00000158669
HPRD : 12175
Vega : OTTHUMG00000164082
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AGPAT6
BioGPS: 137964
Gene Expression Atlas: ENSG00000158669
The Human Protein Atlas: ENSG00000158669
PathwayNCI Pathway Interaction Database: AGPAT6
KEGG: AGPAT6
REACTOME: AGPAT6
ConsensusPathDB
Pathway Commons: AGPAT6
MetabolismMetaCyc: AGPAT6
HUMANCyc: AGPAT6
RegulationEnsembl's Regulation: ENSG00000158669
miRBase: chr8 :41,435,706-41,482,520
TargetScan: NM_178819
cisRED: ENSG00000158669
ContextiHOP: AGPAT6
cancer metabolism search in PubMed: AGPAT6
UCL Cancer Institute: AGPAT6
Assigned class in ccmGDBC

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Phenotypic Information for AGPAT6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AGPAT6
Familial Cancer Database: AGPAT6
* 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_GLYCEROLIPID_METABOLISM
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: AGPAT6
MedGen: AGPAT6 (Human Medical Genetics with Condition)
ClinVar: AGPAT6
PhenotypeMGI: AGPAT6 (International Mouse Phenotyping Consortium)
PhenomicDB: AGPAT6

Mutations for AGPAT6
* 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
breastAGPAT6chr84145783741457837AGPAT6chr84146931841469318
pancreasAGPAT6chr84144376941443789AGPAT6chr84144940041449420
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 AGPAT6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW264211CDK2AP217113116727397267274068AGPAT610959784146973241476461

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 # sample6  3  5 3 1   1 1
GAIN (# sample)5  3  5 2 1   1 1
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr8:41456786-41456786p.R43H4
chr8:41469477-41469477p.R223*3
chr8:41467367-41467367p.W143*2
chr8:41469749-41469749p.P251L2
chr8:41467379-41467379p.S147S2
chr8:41456817-41456817p.I53M2
chr8:41469728-41469728p.C244S1
chr8:41456755-41456755p.P33S1
chr8:41476277-41476277p.M376I1
chr8:41476308-41476308p.Y387H1

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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 2171   31 411  24 6
# mutation 2171   31 411  24 8
nonsynonymous SNV 2141   3  211  22 5
synonymous SNV   3     1 2     2 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
chr8:41456786p.S147S2
chr8:41467379p.R43H2
chr8:41470394p.G99C1
chr8:41467422p.G267C1
chr8:41470463p.D105E1
chr8:41466955p.V276L1
chr8:41467449p.F110F1
chr8:41471927p.H299Y1
chr8:41467214p.K312E1
chr8:41468294p.F116F1

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 AGPAT6 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 AGPAT6

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

AGPAT6,AP3M2,ASH2L,BAG4,BRF2,SMIM19,DDHD2,
FNTA,GINS4,GOLGA7,HGSNAT,IKBKB,KAT6A,POLB,
PTH,RAB11FIP1,RNF170,SLC20A2,THAP1,VDAC3,WHSC1L1
ACBD6,AGPAT6,ALKBH2,CCT3,DDX54,EBNA1BP2,EIF3B,
EXOSC5,MRTO4,NCL,NOP16,PES1,RRP1,RUVBL2,
SHMT2,SMARCA4,SMARCD2,SND1,SURF6,TOP1MT,WDR74

AGPAT6,ANK1,FAM84B,FNTA,GINS4,GLYATL2,GOLGA7,
HGSNAT,HOOK3,IKBKB,IMPAD1,KIAA1429,KAT6A,OR13C4,
RB1CC1,RNF170,SLC20A2,SLC5A8,STXBP5L,TGS1,UBXN2B
AGPAT6,CCDC9,GTF3C1,HIPK2,HTT,IGF2R,KDM2A,
MAVS,MYH9,MYO18A,PTPN23,RNF40,RRBP1,SAFB,
SLC38A1,SMARCA4,UBAP2,UBN1,UPF1,USP7,VPS53
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 AGPAT6


There's no related Drug.
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Cross referenced IDs for AGPAT6
* 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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