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 GNPNAT1
Basic gene info.Gene symbolGNPNAT1
Gene nameglucosamine-phosphate N-acetyltransferase 1
SynonymsGNPNAT|Gpnat1
CytomapUCSC genome browser: 14q22.1
Genomic locationchr14 :53241910-53258386
Type of geneprotein-coding
RefGenesNM_198066.3,
Ensembl idENSG00000100522
Descriptionglucosamine 6-phosphate N-acetyltransferasephosphoglucosamine acetylasephosphoglucosamine transacetylase
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000100522
HPRD : 17046
Vega : OTTHUMG00000152334
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNPNAT1
BioGPS: 64841
Gene Expression Atlas: ENSG00000100522
The Human Protein Atlas: ENSG00000100522
PathwayNCI Pathway Interaction Database: GNPNAT1
KEGG: GNPNAT1
REACTOME: GNPNAT1
ConsensusPathDB
Pathway Commons: GNPNAT1
MetabolismMetaCyc: GNPNAT1
HUMANCyc: GNPNAT1
RegulationEnsembl's Regulation: ENSG00000100522
miRBase: chr14 :53,241,910-53,258,386
TargetScan: NM_198066
cisRED: ENSG00000100522
ContextiHOP: GNPNAT1
cancer metabolism search in PubMed: GNPNAT1
UCL Cancer Institute: GNPNAT1
Assigned class in ccmGDBC

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Phenotypic Information for GNPNAT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GNPNAT1
Familial Cancer Database: GNPNAT1
* 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_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GNPNAT1
MedGen: GNPNAT1 (Human Medical Genetics with Condition)
ClinVar: GNPNAT1
PhenotypeMGI: GNPNAT1 (International Mouse Phenotyping Consortium)
PhenomicDB: GNPNAT1

Mutations for GNPNAT1
* 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 GNPNAT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI904839GNPNAT112415145325690553257308GNPNAT1412466145325764753257701
DW412766GNPNAT117112145325561453255709STYX112323145324143453241645

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=9)
Stat. for Synonymous SNVs
(# total SNVs=2)
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
chr14:53245068-53245068p.V172V2
chr14:53245146-53245146p.K146N2
chr14:53248504-53248504p.K115E1
chr14:53251332-53251332p.L13V1
chr14:53248520-53248520p.F109F1
chr14:53248574-53248608p.K80fs*171
chr14:53250168-53250168p.G64R1
chr14:53250170-53250170p.T63N1
chr14:53245045-53245045p.R180Q1
chr14:53250176-53250176p.T61R1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21 1  1    1       1
# mutation21 1  1    1       1
nonsynonymous SNV11 1  1    1       1
synonymous SNV1                   
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
chr14:53251269p.D18N1
chr14:53251317p.L13V1
chr14:53251332p.R180Q1
chr14:53245045p.K166N1
chr14:53245086p.F109F1
chr14:53248520p.T61R1
chr14:53250176p.L44V1
chr14:53251239p.H34Y1

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 GNPNAT1 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 GNPNAT1

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

ARF6,C14orf166,CNIH1,CTAGE5,DDHD1,EXOC5,FANCM,
GMFB,GNPNAT1,KIAA0391,L2HGDH,NAA30,PPP2R5E,PSMC6,
NEMF,SOCS4,SOS2,STYX,TM9SF3,TMX1,TXNDC16
ABCE1,CNOT6,DHX15,EPT1,GNPNAT1,MRPL42,OAT,
PAICS,PIGN,PPAT,PRKCI,PRRC1,RFC3,RNF2,
PTBP3,SRSF1,SRP72,SRPK1,SSX2IP,SUV39H2,TFAM

ARF6,C14orf166,CDKN3,DLGAP5,DLST,EIF2S1,GLRX5,
GNPNAT1,L2HGDH,MTHFD1,AP5M1,PNP,POLE2,PRMT5,
RPL36AL,SCFD1,TC2N,TMED10,TMX1,VRK1,WDHD1
ABCE1,BRIX1,CCT2,DKC1,EIF4A1,FARSB,GNL3,
GNPNAT1,KIAA0020,METTL1,MRPL3,NOP58,PAICS,POLR1C,
PRDX4,PYCRL,SRFBP1,SRPRB,SUV39H2,UBXN8,WDR77
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 GNPNAT1


There's no related Drug.
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Cross referenced IDs for GNPNAT1
* 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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