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 NNMT
Basic gene info.Gene symbolNNMT
Gene namenicotinamide N-methyltransferase
Synonyms-
CytomapUCSC genome browser: 11q23.1
Genomic locationchr11 :114166534-114183238
Type of geneprotein-coding
RefGenesNM_006169.2,
Ensembl idENSG00000166741
Description-
Modification date20141207
dbXrefs MIM : 600008
HGNC : HGNC
Ensembl : ENSG00000166741
HPRD : 02478
Vega : OTTHUMG00000168245
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NNMT
BioGPS: 4837
Gene Expression Atlas: ENSG00000166741
The Human Protein Atlas: ENSG00000166741
PathwayNCI Pathway Interaction Database: NNMT
KEGG: NNMT
REACTOME: NNMT
ConsensusPathDB
Pathway Commons: NNMT
MetabolismMetaCyc: NNMT
HUMANCyc: NNMT
RegulationEnsembl's Regulation: ENSG00000166741
miRBase: chr11 :114,166,534-114,183,238
TargetScan: NM_006169
cisRED: ENSG00000166741
ContextiHOP: NNMT
cancer metabolism search in PubMed: NNMT
UCL Cancer Institute: NNMT
Assigned class in ccmGDBC

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

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

Mutations for NNMT
* 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 NNMT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF913499TERF27471166940450569419618NNMT46457411114182954114183064

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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=32)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr11:114183101-114183101p.E233K5
chr11:114168780-114168780p.D88N3
chr11:114183152-114183152p.E250K2
chr11:114182863-114182863p.P153P2
chr11:114168875-114168875p.G119G2
chr11:114167282-114167282p.E2K1
chr11:114182820-114182820p.L139P1
chr11:114167428-114167428p.C50C1
chr11:114182997-114182997p.A198V1
chr11:114168772-114168772p.D85G1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  61 1 1  911  123 6
# mutation1  61 1 1  1011  113 6
nonsynonymous SNV1  4  1 1  7 1  71 4
synonymous SNV   21      31   42 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
chr11:114183101p.E233K4
chr11:114183152p.G119G2
chr11:114168875p.E250K2
chr11:114167310p.E80K1
chr11:114182998p.V194V1
chr11:114168716p.I81I1
chr11:114182844p.A198V1
chr11:114167333p.Y11C1
chr11:114183018p.D85G1
chr11:114168749p.A198A1

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 NNMT 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 NNMT

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

CLEC11A,COPZ2,EFEMP2,EMP3,LDLRAD2,LGALS1,LOC100270710,
LOC541471,MFRP,MYL9,NNMT,PDLIM7,PLAC9,PODNL1,
PPAPDC3,PTGIR,PTRF,RARRES2,TGFB1I1,THY1,TPM2
A4GALT,BATF3,C10orf54,SMIM12,C1R,CEBPD,ACKR1,
FAM107A,HYAL2,IFITM2,IFITM3,ITGA5,LOC541471,METRNL,
MT1M,NNMT,VIMP,TAGLN2,TMEM173,TMSB4XP8,TNFRSF1A

MEDAG,C1R,CFH,CNRIP1,COL6A2,COPZ2,EFEMP2,
ENG,FNDC4,GYPC,HSPB2,KCNE4,MRAS,NNMT,
NRP1,PECAM1,PTRF,SEMA6B,SERPING1,TSPAN4,VIM
ABCE1,ABRA,ARID5A,BRIX1,AAED1,CREM,CYP19A1,
DYRK3,EIF2S1,HYAL2,IL1R1,IL1RL1,LRRC70,MAK16,
NNMT,NXT1,PDPN,S100A9,SLC25A32,SOCS3,STEAP4
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 NNMT
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
DB00627nicotinamide N-methyltransferaseapproved; nutraceutical; investigationalNiacin
DB00640nicotinamide N-methyltransferaseapproved; investigationalAdenosine
DB00134nicotinamide N-methyltransferaseapproved; nutraceuticalL-Methionine
DB00158nicotinamide N-methyltransferaseapproved; nutraceuticalFolic Acid


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Cross referenced IDs for NNMT
* 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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