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 NAGS
Basic gene info.Gene symbolNAGS
Gene nameN-acetylglutamate synthase
SynonymsAGAS|ARGA
CytomapUCSC genome browser: 17q21.31
Genomic locationchr17 :42082031-42086436
Type of geneprotein-coding
RefGenesNM_153006.2,
Ensembl idENSG00000161653
DescriptionN-acetylglutamate synthase, mitochondrialamino-acid acetyltransferase
Modification date20141207
dbXrefs MIM : 608300
HGNC : HGNC
Ensembl : ENSG00000161653
HPRD : 10510
Vega : OTTHUMG00000181802
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NAGS
BioGPS: 162417
Gene Expression Atlas: ENSG00000161653
The Human Protein Atlas: ENSG00000161653
PathwayNCI Pathway Interaction Database: NAGS
KEGG: NAGS
REACTOME: NAGS
ConsensusPathDB
Pathway Commons: NAGS
MetabolismMetaCyc: NAGS
HUMANCyc: NAGS
RegulationEnsembl's Regulation: ENSG00000161653
miRBase: chr17 :42,082,031-42,086,436
TargetScan: NM_153006
cisRED: ENSG00000161653
ContextiHOP: NAGS
cancer metabolism search in PubMed: NAGS
UCL Cancer Institute: NAGS
Assigned class in ccmGDBC

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Phenotypic Information for NAGS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NAGS
Familial Cancer Database: NAGS
* 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_ARGININE_AND_PROLINE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for NAGS
* 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 NAGS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
R97030NAGS195174208633242086426LIN548537448386882083869103

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
There's no copy number variation information in COSMIC data for this gene.

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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=17)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr17:42082082-42082082p.P17P2
chr17:42085912-42085912p.N516K2
chr17:42082139-42082139p.R36R2
chr17:42083553-42083553p.T288I2
chr17:42083115-42083115p.A179A2
chr17:42082046-42082046p.L5L1
chr17:42083122-42083122p.A182T1
chr17:42085843-42085843p.F493L1
chr17:42082049-42082049p.M6I1
chr17:42083124-42083124p.A182A1

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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   61 3 11 31  1 3 3
# mutation   61 3 11 31  1 3 3
nonsynonymous SNV   51 2  1  1    1 3
synonymous SNV   1  1 1  3   1 2  
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
chr17:42082046p.M6I1
chr17:42083544p.G491G1
chr17:42085958p.A14D1
chr17:42082049p.F493L1
chr17:42083545p.P17P1
chr17:42082072p.F501L1
chr17:42084041p.A35A1
chr17:42082082p.N516K1
chr17:42084701p.F163V1
chr17:42082136p.A518T1

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 NAGS 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 NAGS

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

C12orf60,ERLIN2,G6PC3,GABRA1,H2AFJ,NAGS,LINC00176,
NPEPL1,RBMY1A3P,RBMY1E,RBMY1F,RBMY1J,RBMY2FP,RBMY3AP,
SSTR1,TCEAL1,TCEAL3,TCEAL6,TMEM101,TSPY1,ZNF703
BEX2,C10orf35,DDR1,EPHA1,FAAH2,GGT7,GLS2,
HKR1,IP6K2,LYPD6B,MED29,MPP2,NAGS,PAK6,
PRKCZ,PSD4,RAB17,SEMA4B,SH2D3A,TNK1,VSIG2

TMEM253,SSUH2,CACNA2D4,CDA,CEACAM18,CEACAM20,EMX1,
ITPKA,LACTB2,MBOAT7,MTTP,NAGS,NLRP6,REEP6,
SLC46A3,SLC6A20,SLC7A9,TM4SF20,TM6SF2,TMEM45B,ABHD11-AS1
ALPI,ADIRF,TMEM253,CHN2,CYP2J2,DGAT1,FADS6,
SLC52A1,HEBP1,MMEL1,NAGS,OIT3,PCK2,PGRMC2,
PKLR,PLA2G12B,SLC15A1,SLC5A11,SLC6A19,TM4SF5,TMPRSS7
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 NAGS
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00142N-acetylglutamate synthaseapproved; nutraceuticalL-Glutamic Acid
DB00125N-acetylglutamate synthaseapproved; nutraceuticalL-Arginine
DB03904N-acetylglutamate synthaseexperimentalUrea


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Cross referenced IDs for NAGS
* 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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