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 NMNAT2
Basic gene info.Gene symbolNMNAT2
Gene namenicotinamide nucleotide adenylyltransferase 2
SynonymsC1orf15|PNAT2
CytomapUCSC genome browser: 1q25
Genomic locationchr1 :183217371-183387634
Type of geneprotein-coding
RefGenesNM_015039.3,
NM_170706.3,
Ensembl idENSG00000157064
DescriptionNMN adenylyltransferase 2NaMN adenylyltransferase 2nicotinamide mononucleotide adenylyltransferase 2nicotinate-nucleotide adenylyltransferase 2pyridine nucleotide adenylyltransferase 2
Modification date20141207
dbXrefs MIM : 608701
HGNC : HGNC
Ensembl : ENSG00000157064
HPRD : 09786
Vega : OTTHUMG00000035519
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NMNAT2
BioGPS: 23057
Gene Expression Atlas: ENSG00000157064
The Human Protein Atlas: ENSG00000157064
PathwayNCI Pathway Interaction Database: NMNAT2
KEGG: NMNAT2
REACTOME: NMNAT2
ConsensusPathDB
Pathway Commons: NMNAT2
MetabolismMetaCyc: NMNAT2
HUMANCyc: NMNAT2
RegulationEnsembl's Regulation: ENSG00000157064
miRBase: chr1 :183,217,371-183,387,634
TargetScan: NM_015039
cisRED: ENSG00000157064
ContextiHOP: NMNAT2
cancer metabolism search in PubMed: NMNAT2
UCL Cancer Institute: NMNAT2
Assigned class in ccmGDBC

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Phenotypic Information for NMNAT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NMNAT2
Familial Cancer Database: NMNAT2
* 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: NMNAT2
MedGen: NMNAT2 (Human Medical Genetics with Condition)
ClinVar: NMNAT2
PhenotypeMGI: NMNAT2 (International Mouse Phenotyping Consortium)
PhenomicDB: NMNAT2

Mutations for NMNAT2
* 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
ovaryNMNAT2chr1183230950183230970chr1182930055182930075
ovaryNMNAT2chr1183245960183245980NMNAT2chr1183246012183246032
ovaryNMNAT2chr1183330104183330124chr181121311233
ovaryNMNAT2chr1183330253183330273chr205722083757220857
ovaryNMNAT2chr1183378265183378285chr1182730278182730298
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 NMNAT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CN288204FUS2440163119146831195568NMNAT24345381183218278183218381
AK126960UNC13C12048155438608754388134NMNAT2204127371183217373183218069

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 # sample3 1       1      
GAIN (# sample)3 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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=37)
Stat. for Synonymous SNVs
(# total SNVs=15)
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
chr1:183221856-183221856p.G282S4
chr1:183253160-183253160p.L182M3
chr1:183262858-183262858p.H52H3
chr1:183230397-183230397p.P231P2
chr1:183259275-183259275p.R103R2
chr1:183253905-183253905p.G157R2
chr1:183387360-183387360p.G15C2
chr1:183230196-183230196p.I254M2
chr1:183255852-183255852p.N131N2
chr1:183230359-183230359p.S244F2

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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 1 61 1 1 1821  42 6
# mutation 1 61 1 1 1831  42 5
nonsynonymous SNV 1 5    1 1621  32 3
synonymous SNV   11 1    21   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
chr1:183262858p.H52H,NMNAT22
chr1:183255900p.A180V,NMNAT22
chr1:183253165p.S115S,NMNAT22
chr1:183221856p.G282S,NMNAT22
chr1:183253881p.V256V,NMNAT21
chr1:183230190p.V82L,NMNAT21
chr1:183253890p.S244Y,NMNAT21
chr1:183262892p.A73A,NMNAT21
chr1:183230359p.R232Q,NMNAT21
chr1:183253906p.R66H,NMNAT21

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 NMNAT2 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 NMNAT2

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

AP3B2,APLP1,BSN,CHRNB2,DDX25,AMER3,GNAO1,
UNC79,NMNAT2,PCDH9,RAB34___RAB39A,RIPPLY2,RUNDC3A,SCG3,
SCN3B,SNAP25,SYN1,SYP,SYT4,TMEM145,UNC13A
ANO6,ARHGAP31,BTNL9,PQLC2L,CAT,CD300LG,CRYBG3,
EBF1,FERMT2,GJC1,HSD17B13,KCNIP2,KIAA1462,NMNAT2,
PDE3B,PDE8A,PPP2R5A,SH3KBP1,SIK2,STXBP1,TYRO3

BSN,CAMKV,ERC2,AMER3,GRM4,KCNC1,KCNH6,
LOC254559,NMNAT2,PRMT8,RAB3C,RPRML,SCG3,SCN3B,
SLC6A15,SNAP25,SVOP,SYP,SLC35G2,VGF,XKR7
ANK2,ARHGAP6,C20orf194,CDON,FAM129A,FAM131B,HDAC4,
ITPKB,MTCL1,LONRF2,MASP1,MYOCD,NMNAT2,NRXN1,
PRDM6,PTCHD1,SSC5D,WBSCR17,WHAMMP3,ZBTB47,ZMAT4
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 NMNAT2
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
DB00160nicotinamide nucleotide adenylyltransferase 2approved; nutraceuticalL-Alanine
DB00130nicotinamide nucleotide adenylyltransferase 2approved; nutraceutical; investigationalL-Glutamine
DB00150nicotinamide nucleotide adenylyltransferase 2approved; nutraceuticalL-Tryptophan


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Cross referenced IDs for NMNAT2
* 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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