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 GNPAT
Basic gene info.Gene symbolGNPAT
Gene nameglyceronephosphate O-acyltransferase
SynonymsDAP-AT|DAPAT|DHAPAT
CytomapUCSC genome browser: 1q42
Genomic locationchr1 :231376918-231413719
Type of geneprotein-coding
RefGenesNM_014236.3,
Ensembl idENSG00000116906
DescriptionDHAP-ATacyl-CoA:dihydroxyacetonephosphateacyltransferasedihydroxyacetone phosphate acyltransferaseglycerone-phosphate O-acyltransferase
Modification date20141207
dbXrefs MIM : 602744
HGNC : HGNC
Ensembl : ENSG00000116906
HPRD : 04120
Vega : OTTHUMG00000038024
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNPAT
BioGPS: 8443
Gene Expression Atlas: ENSG00000116906
The Human Protein Atlas: ENSG00000116906
PathwayNCI Pathway Interaction Database: GNPAT
KEGG: GNPAT
REACTOME: GNPAT
ConsensusPathDB
Pathway Commons: GNPAT
MetabolismMetaCyc: GNPAT
HUMANCyc: GNPAT
RegulationEnsembl's Regulation: ENSG00000116906
miRBase: chr1 :231,376,918-231,413,719
TargetScan: NM_014236
cisRED: ENSG00000116906
ContextiHOP: GNPAT
cancer metabolism search in PubMed: GNPAT
UCL Cancer Institute: GNPAT
Assigned class in ccmGDBC

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

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

Mutations for GNPAT
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryGNPATchr1231396783231396803chr98373147583731495
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 GNPAT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA174856PLP11103X103031789103031891GNPAT1025261231410993231413439
AW810786GNPAT62101231393186231393390GNPAT2035341231392635231392966
AK023953NFIA58687016192669561926976GNPAT87127741231398550231413668

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
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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=67)
Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=2)

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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
chr1:231408064-231408064p.V510A5
chr1:231408063-231408063p.V510I3
chr1:231403468-231403468p.V366V2
chr1:231411174-231411174p.L623V2
chr1:231398518-231398518p.R163Q2
chr1:231406610-231406610p.S462S2
chr1:231401902-231401902p.E305E2
chr1:231401908-231401908p.T307T2
chr1:231401795-231401795p.R270G2
chr1:231411021-231411021p.Y600H2

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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=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 51141 2 2  923 132210
# mutation 5191 2 2  923 132215
nonsynonymous SNV 3191 2 2  623 122211
synonymous SNV 2         3    1  4
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
chr1:231408064p.V510A5
chr1:231403468p.R270G2
chr1:231406610p.S462S2
chr1:231401795p.V366V2
chr1:231408129p.Y541C1
chr1:231398578p.G193G1
chr1:231402043p.W386C1
chr1:231406513p.K554R1
chr1:231386845p.N8D1
chr1:231409687p.F207L1

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 GNPAT 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 GNPAT

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

AHCTF1,AIDA,ARV1,SPRTN,C1orf131,COG2,EXOC8,
FBXO28,FH,GGPS1,GNPAT,NUP133,RAB4A,RBM34,
RFWD2,SRP9,TAF5L,TBCE,TFB2M,TOMM20,TSNAX
ACAT1,AK3,ATPAF1,TCAIM,CSDE1,DLD,GHITM,
GKAP1,GNPAT,HADHB,HOXA10,HSPB6,ISCA1P1,NRD1,
PGM1,PHYH,PPP3CB,RRAGD,SETD3,SUCLA2,TBX15

ARF1,SPRTN,C1orf131,C1orf27,C1orf43,COG2,GGPS1,
GNPAT,MRPS14,NUP133,POLR3C,RAB3GAP2,RAB4A,RBM34,
RCOR3,TATDN3,TBCE,TIPRL,TOMM20,TSNAX,UFC1
ARL3,CAMLG,CBY1,CRYZL1,EIF4A2,ELP2,FAM172A,
FAM175A,MTFR1L,GNPAT,H2AFV,HIBADH,ISCU,LZTFL1,
MEAF6,MFF,CMC4,POLR1D,RYK,TTC33,ZNF639
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 GNPAT


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