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 NMNAT3
Basic gene info.Gene symbolNMNAT3
Gene namenicotinamide nucleotide adenylyltransferase 3
SynonymsPNAT-3|PNAT3
CytomapUCSC genome browser: 3q23
Genomic locationchr3 :139279022-139396885
Type of geneprotein-coding
RefGenesNM_001200047.1,
NM_178177.3,
Ensembl idENSG00000163864
DescriptionNMN adenylyltransferase 3NaMN adenylyltransferase 3nicotinamide mononucleotide adenylyltransferase 3nicotinate-nucleotide adenylyltransferase 3pyridine nucleotide adenylyltransferase 3
Modification date20141207
dbXrefs MIM : 608702
HGNC : HGNC
Ensembl : ENSG00000163864
HPRD : 16370
Vega : OTTHUMG00000159951
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NMNAT3
BioGPS: 349565
Gene Expression Atlas: ENSG00000163864
The Human Protein Atlas: ENSG00000163864
PathwayNCI Pathway Interaction Database: NMNAT3
KEGG: NMNAT3
REACTOME: NMNAT3
ConsensusPathDB
Pathway Commons: NMNAT3
MetabolismMetaCyc: NMNAT3
HUMANCyc: NMNAT3
RegulationEnsembl's Regulation: ENSG00000163864
miRBase: chr3 :139,279,022-139,396,885
TargetScan: NM_001200047
cisRED: ENSG00000163864
ContextiHOP: NMNAT3
cancer metabolism search in PubMed: NMNAT3
UCL Cancer Institute: NMNAT3
Assigned class in ccmGDBC

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Phenotypic Information for NMNAT3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NMNAT3
Familial Cancer Database: NMNAT3
* 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_NICOTINATE_AND_NICOTINAMIDE_METABOLISM
REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NMNAT3
MedGen: NMNAT3 (Human Medical Genetics with Condition)
ClinVar: NMNAT3
PhenotypeMGI: NMNAT3 (International Mouse Phenotyping Consortium)
PhenomicDB: NMNAT3

Mutations for NMNAT3
* 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
* 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
breastNMNAT3chr3139336883139336883NMNAT3chr3139341805139341805
ovaryNMNAT3chr3139322055139322075CDH12chr52280923922809259
ovaryNMNAT3chr3139332939139332959chr83356467833564698
pancreasNMNAT3chr3139302618139302638NMNAT3chr3139302328139302348
pancreasNMNAT3chr3139352683139352703NMNAT3chr3139354170139354190
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 NMNAT3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF576138CCDC3625034923695849237006NMNAT3496193139279664139280236
BM544763MAG16136193578513835786353NMNAT31378773139279838139396595

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        
GAIN (# sample)        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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=12)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr3:139297857-139297857p.N13N3
chr3:139297737-139297737p.W53*3
chr3:139297773-139297773p.I41I2
chr3:139279867-139279867p.E211D2
chr3:139297817-139297817p.R27*2
chr3:139297832-139297832p.A22T1
chr3:139279987-139279987p.A171A1
chr3:139297746-139297746p.Q50Q1
chr3:139297845-139297845p.G17G1
chr3:139279992-139279992p.R170*1

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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   21   1  22   112  
# mutation   21   1  22   132  
nonsynonymous SNV   2    1  11   61  
synonymous SNV    1      11   71  
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
chr3:139297773p.I41I2
chr3:139279987p.V76M,NMNAT31
chr3:139297856p.Q65R,NMNAT31
chr3:139280028p.Q73Q1
chr3:139297857p.A51V1
chr3:139280118p.Q50Q1
chr3:139297865p.P45P1
chr3:139280150p.Q36H1
chr3:139297868p.G17G1
chr3:139292486p.E159D,NMNAT31

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 NMNAT3 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 NMNAT3

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

ASB13,BCL2,CLSTN2,DBNDD2,DCAKD,DNALI1,FAM110B,
FUZ,GATA3,KDM4B,LOC100190938,LOC284440,LYPD6,LYPD6B,
MYB,MYOZ3,NMNAT3,STK32B,TLE3,TMEM26,TRIM45
AKAP1,ANAPC16,CNBP,FAF1,FBXO42,HADHA,LIAS,
MCEE,NDUFS4,NMNAT3,OXA1L,POLR2C,SAMM50,SCMH1,
SLC25A23,SLC25A26,SLC25A42,SRP68,TARSL2,UQCRC2,VDAC2

ASPSCR1,AXIN2,BAMBI,CAB39L,DACH1,DDX31,KRT32,
KRT35,LINC01512,MSX2,MSX2P1,NCKAP5,NMNAT3,KIZ,
RPL12,SESN1,SNTB1,SP5,SYK,TCEAL1,TCF7
AGBL5,FAM210B,DHX40,DVL2,GAL3ST4,GNPAT,LOC284023,
LOC400027,MBTPS1,EPB41L4A-AS1,NMNAT3,POLL,PPOX,SLC41A3,
SNAP47,TAB1,TRAK2,YPEL1,ZDHHC1,ZNF345,ZNF559
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 NMNAT3
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
DB01907nicotinamide nucleotide adenylyltransferase 3experimentalNicotinamide-Adenine-Dinucleotide
DB02596nicotinamide nucleotide adenylyltransferase 3experimentalAlpha,Beta-Methyleneadenosine-5'-Triphosphate
DB03227nicotinamide nucleotide adenylyltransferase 3experimentalNicotinamide Mononucleotide
DB04099nicotinamide nucleotide adenylyltransferase 3experimentalDeamido-Nad+
DB00160nicotinamide nucleotide adenylyltransferase 3approved; nutraceuticalL-Alanine
DB00130nicotinamide nucleotide adenylyltransferase 3approved; nutraceutical; investigationalL-Glutamine
DB00150nicotinamide nucleotide adenylyltransferase 3approved; nutraceuticalL-Tryptophan


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Cross referenced IDs for NMNAT3
* 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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