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 NMNAT1
Basic gene info.Gene symbolNMNAT1
Gene namenicotinamide nucleotide adenylyltransferase 1
SynonymsLCA9|NMNAT|PNAT1
CytomapUCSC genome browser: 1p36.22
Genomic locationchr1 :10003485-10045556
Type of geneprotein-coding
RefGenesNM_001297778.1,
NM_001297779.1,NM_022787.3,
Ensembl idENSG00000173614
DescriptionNMN adenylyltransferase 1NaMN adenylyltransferase 1nicotinamide mononucleotide adenylyltransferase 1nicotinate-nucleotide adenylyltransferase 1pyridine nucleotide adenylyltransferase 1
Modification date20141207
dbXrefs MIM : 608700
HGNC : HGNC
Ensembl : ENSG00000173614
HPRD : 16369
Vega : OTTHUMG00000001799
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NMNAT1
BioGPS: 64802
Gene Expression Atlas: ENSG00000173614
The Human Protein Atlas: ENSG00000173614
PathwayNCI Pathway Interaction Database: NMNAT1
KEGG: NMNAT1
REACTOME: NMNAT1
ConsensusPathDB
Pathway Commons: NMNAT1
MetabolismMetaCyc: NMNAT1
HUMANCyc: NMNAT1
RegulationEnsembl's Regulation: ENSG00000173614
miRBase: chr1 :10,003,485-10,045,556
TargetScan: NM_001297778
cisRED: ENSG00000173614
ContextiHOP: NMNAT1
cancer metabolism search in PubMed: NMNAT1
UCL Cancer Institute: NMNAT1
Assigned class in ccmGDBC

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Phenotypic Information for NMNAT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NMNAT1
Familial Cancer Database: NMNAT1
* 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: NMNAT1
MedGen: NMNAT1 (Human Medical Genetics with Condition)
ClinVar: NMNAT1
PhenotypeMGI: NMNAT1 (International Mouse Phenotyping Consortium)
PhenomicDB: NMNAT1

Mutations for NMNAT1
* 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 NMNAT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BJ997860SMA4130057022088970237320NMNAT129560011004439210044697
BQ372419TPM110290156334859563349095NMNAT127230111000904610009075

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=15)
Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr1:10042579-10042579p.D220E2
chr1:10042450-10042450p.I177I1
chr1:10042683-10042683p.S255N1
chr1:10032143-10032143p.S4S1
chr1:10042464-10042464p.G182E1
chr1:10042714-10042714p.V265V1
chr1:10032227-10032227p.K32K1
chr1:10042475-10042475p.V186I1
chr1:10035735-10035735p.V67V1
chr1:10042490-10042490p.N191D1

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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 112  3    4    12 5
# mutation 112  3    4    12 5
nonsynonymous SNV 1 2  3    3     1 3
synonymous SNV  1        1    11 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
chr1:10041203p.N191D1
chr1:10032143p.V212M1
chr1:10042404p.S4S1
chr1:10032227p.S222L1
chr1:10042450p.K32K1
chr1:10032236p.K250N1
chr1:10042464p.M35I1
chr1:10035738p.V265V1
chr1:10042490p.I68I1
chr1:10035759p.K75N1

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 NMNAT1 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 NMNAT1

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

DNAJC16,EXOSC10,FBXO42,GNB1,HMGCL,ICMT,CEP104,
LZIC,MED18,MFN2,MTHFR,MTOR,NMNAT1,PHACTR4,
PRDM2,RERE,SLC35E2,UBE4B,USP48,VPS13D,ZBTB40
ALDH5A1,CUL4A,FECH,HBS1L,KLHL31,LOC729082,LYRM7,
NDUFS1,NMNAT1,NNT,PCBD2,PDHX,PRKAB2,PRKAR2A,
PTCD3,RHOBTB1,SGCD,UBR3,USO1,ZNF106,ZYG11B

ABCD3,ATP5F1,MPC1,MINOS1,CDC42,DNAJC11,DNAJC16,
ETFDH,FUCA1,HADH,HMGCL,LZIC,MED18,NMNAT1,
OMA1,PAFAH2,PGD,PXMP2,SDHB,SLC35A3,TMEM106C
AIMP2,ALG14,BPNT1,MPC1,TMEM251,C15orf48,ABRACL,
MICU2,ETFA,FAM195A,LGALS3,MGST3,MLX,NMNAT1,
NRAS,SLC25A16,SLMO2,SRI,UOX,UQCRC2,UQCRFS1
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 NMNAT1
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 1experimentalNicotinamide-Adenine-Dinucleotide
DB03227nicotinamide nucleotide adenylyltransferase 1experimentalNicotinamide Mononucleotide
DB04099nicotinamide nucleotide adenylyltransferase 1experimentalDeamido-Nad+
DB00160nicotinamide nucleotide adenylyltransferase 1approved; nutraceuticalL-Alanine
DB00130nicotinamide nucleotide adenylyltransferase 1approved; nutraceutical; investigationalL-Glutamine
DB00150nicotinamide nucleotide adenylyltransferase 1approved; nutraceuticalL-Tryptophan


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Cross referenced IDs for NMNAT1
* 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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