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 NAT2
Basic gene info.Gene symbolNAT2
Gene nameN-acetyltransferase 2 (arylamine N-acetyltransferase)
SynonymsAAC2|NAT-2|PNAT
CytomapUCSC genome browser: 8p22
Genomic locationchr8 :18248754-18258723
Type of geneprotein-coding
RefGenesNM_000015.2,
Ensembl idENSG00000156006
DescriptionN-acetyltransferase type 2arylamide acetylase 2arylamine N-acetyltransferase 2
Modification date20141211
dbXrefs MIM : 612182
HGNC : HGNC
Ensembl : ENSG00000156006
HPRD : 02000
Vega : OTTHUMG00000130826
ProteinUniProt: P11245
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NAT2
BioGPS: 10
Gene Expression Atlas: ENSG00000156006
The Human Protein Atlas: ENSG00000156006
PathwayNCI Pathway Interaction Database: NAT2
KEGG: NAT2
REACTOME: NAT2
ConsensusPathDB
Pathway Commons: NAT2
MetabolismMetaCyc: NAT2
HUMANCyc: NAT2
RegulationEnsembl's Regulation: ENSG00000156006
miRBase: chr8 :18,248,754-18,258,723
TargetScan: NM_000015
cisRED: ENSG00000156006
ContextiHOP: NAT2
cancer metabolism search in PubMed: NAT2
UCL Cancer Institute: NAT2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NAT2 in cancer cell metabolism1. Matejcic M, Vogelsang M, Wang Y, Parker M (2015) NAT1 and NAT2 genetic polymorphisms and environmental exposure as risk factors for oesophageal squamous cell carcinoma: a case-control study. BMC cancer 15: 150. go to article

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Phenotypic Information for NAT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NAT2
Familial Cancer Database: NAT2
* 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_DRUG_METABOLISM_OTHER_ENZYMES

check002.gifOthers
OMIM 243400; phenotype.
243400; phenotype.
612182; gene.
612182; gene.
Orphanet 240887; Isoniazid toxicity.
240887; Isoniazid toxicity.
240975; Susceptibility to adverse reaction due to isoniazide treatment.
240975; Susceptibility to adverse reaction due to isoniazide treatment.
DiseaseKEGG Disease: NAT2
MedGen: NAT2 (Human Medical Genetics with Condition)
ClinVar: NAT2
PhenotypeMGI: NAT2 (International Mouse Phenotyping Consortium)
PhenomicDB: NAT2

Mutations for NAT2
* 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
ovaryNAT2chr81825495218254972chr81824477218244792
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 NAT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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)    1            
LOSS (# sample)      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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=25)
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
chr8:18258334-18258334p.S274F3
chr8:18257858-18257858p.D115D3
chr8:18257539-18257539p.R9I3
chr8:18258273-18258273p.E254K2
chr8:18257994-18257994p.L161L2
chr8:18257673-18257673p.A54T2
chr8:18258186-18258186p.L225L2
chr8:18257864-18257864p.R117R2
chr8:18257721-18257721p.Q70*2
chr8:18258245-18258245p.F244L2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   71   2  412  106 3
# mutation   52   2  412  106 3
nonsynonymous SNV   22   2  211  54 3
synonymous SNV   3       2 1  52  
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
chr8:18257539p.R9K3
chr8:18258186p.D115D2
chr8:18257576p.S274F2
chr8:18257673p.L21F2
chr8:18258334p.A54T2
chr8:18257858p.L225L2
chr8:18257561p.S102S1
chr8:18257862p.T259A1
chr8:18258187p.E260G1
chr8:18257912p.R117W1

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 NAT2 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 NAT2

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

ASAH1,LINC00589,CCDC60,CCDC74A,CYP4A11,DCST1,FAM120AOS,
FAM181B,FDXACB1,MAP10,KRT40,KRTAP1-3,KRTAP3-2,KRTAP3-3,
MBOAT2,MIPOL1,NAT2,PRCP,RBM11,ZNRF3,ZPLD1
ACSL3,ADAM2,ALOX15B,APOD,DHRS2,ENPP3,GUSB,
HAAO,IDI1,NANOG,NAT2,PNLIPRP3,PPEF1,RNASE12,
SERHL2,SERHL,SLC15A1,SPINK8,SULT1C3,UGT2B10,UGT2B11

C10orf99,METTL25,AXDND1,CCDC25,CNOT7,DMTN,EPHX2,
ERICH1,FABP1,FBXO25,FDFT1,GGT6,INTS10,INTS9,
LONRF1,MCPH1,NAT1,NAT2,PEX11A,PPP1R14D,TTC38
ABCD3,BPNT1,ABRACL,CRYL1,CTAGE5,ETFDH,FDX1,
GNG12,MGST3,NAT2,NRAS,SLC51B,PAFAH2,SLC25A20,
SLC35D2,SLC35F5,SNX14,SPPL2A,TGFA,TMEM139,VTA1
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 NAT2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2194; -.
ChemistryChEMBL CHEMBL2194; -.
Organism-specific databasesPharmGKB PA18; -.
Organism-specific databasesPharmGKB PA18; -.
Organism-specific databasesCTD 10; -.
Organism-specific databasesCTD 10; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01248N-acetyltransferase 2 (arylamine N-acetyltransferase)approved; investigationalDocetaxel
DB01041N-acetyltransferase 2 (arylamine N-acetyltransferase)approved; withdrawn; investigationalThalidomide
DB00250N-acetyltransferase 2 (arylamine N-acetyltransferase)approved; investigationalDapsone
DB01068N-acetyltransferase 2 (arylamine N-acetyltransferase)illicit; approvedClonazepam
DB00951N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedIsoniazid
DB00259N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedSulfanilamide
DB00945N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedAcetylsalicylic acid
DB00277N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedTheophylline
DB00898N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedEthanol
DB01412N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedTheobromine
DB00286N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedConjugated Estrogens
DB00201N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedCaffeine
DB00811N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedRibavirin
DB00514N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedDextromethorphan
DB01582N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedSulfamethazine
DB00563N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedMethotrexate
DB00795N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedSulfasalazine
DB01015N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedSulfamethoxazole
DB01035N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedProcainamide
DB01275N-acetyltransferase 2 (arylamine N-acetyltransferase)approvedHydralazine


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Cross referenced IDs for NAT2
* 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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