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 PNMT
Basic gene info.Gene symbolPNMT
Gene namephenylethanolamine N-methyltransferase
SynonymsPENT|PNMTase
CytomapUCSC genome browser: 17q12
Genomic locationchr17 :37824506-37826728
Type of geneprotein-coding
RefGenesNM_002686.4,
NR_073461.1,
Ensembl idENSG00000141744
Descriptionnoradrenaline N-methyltransferasephenylethanolamine N-methylase
Modification date20141207
dbXrefs MIM : 171190
HGNC : HGNC
HPRD : 07176
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PNMT
BioGPS: 5409
Gene Expression Atlas: ENSG00000141744
The Human Protein Atlas: ENSG00000141744
PathwayNCI Pathway Interaction Database: PNMT
KEGG: PNMT
REACTOME: PNMT
ConsensusPathDB
Pathway Commons: PNMT
MetabolismMetaCyc: PNMT
HUMANCyc: PNMT
RegulationEnsembl's Regulation: ENSG00000141744
miRBase: chr17 :37,824,506-37,826,728
TargetScan: NM_002686
cisRED: ENSG00000141744
ContextiHOP: PNMT
cancer metabolism search in PubMed: PNMT
UCL Cancer Institute: PNMT
Assigned class in ccmGDBC

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

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

Mutations for PNMT
* 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 PNMT 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   2  
GAIN (# sample)          1   2  
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=10)		Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=1)		Stat. for Insertions
(# total SNVs=1)

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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
chr17:37826401-37826401p.T203M2
chr17:37824917-37824917p.Q63H2
chr17:37826527-37826527p.R245H2
chr17:37825897-37825897p.R73H2
chr17:37826360-37826360p.P189P2
chr17:37826577-37826577p.L262F1
chr17:37825990-37825990p.E104G1
chr17:37826411-37826411p.R206R1
chr17:37826627-37826627p.Q278H1
chr17:37825994-37825994p.V105V1

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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 2  2 1  131  58 1
# mutation 1 2  2 1  131  57 1
nonsynonymous SNV   2  1     2   47 1
synonymous SNV 1    1 1  111  1   
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
chr17:37826360p.P189P2
chr17:37826401p.T203M2
chr17:37826511p.A149V1
chr17:37826226p.P164H1
chr17:37826527p.A181V1
chr17:37826227p.D199H1
chr17:37826571p.R33H1
chr17:37826239p.S220L1
chr17:37826577p.R37R1
chr17:37824826p.V232V1

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 PNMT 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 PNMT

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

ARHGAP8,BMS1,DDIT4,DHRS2,HIST1H1D,HIST1H2BM,IFT20,
KRT26,KRTAP4-1,LAS1L,LOC146481,NME1,PNMT,POLDIP2,
SEC14L2,TCAP,TLCD1,TMEM199,TNFAIP1,TYSND1,ZNF689		AMPH,CALML3,CDSN,CWH43,CYP4F22,DIO2,DLX1,
DNAJB3,FOXL2,HMGB4,KRTAP15-1,KRTAP5-5,LOC286359,MEPE,
OR10G8,OR4P4,PNMT,SLC18A3,TNFSF11,WNT4,ZNF689

ADAMTSL2,AMBN,CACNA1S,CST5,DBH,DLX3,FGF8,
KLK14,KRT31,LIPM,MYH7B,NELL2,PNMT,RASL11B,
RPTN,S100A3,SERPINI1,SEZ6L,TCHHL1,TSG1,TULP2		ADRA2B,APOD,CA5B,CACNG4,CELF3,CPLX2,CPNE4,
CYP4B1,FAM107A,FKBP5,GAL,KLF15,MCHR2,PDK4,
PNMT,SCG2,SCGN,SCNN1G,SELV,SLC7A2,ZBTB16
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 PNMT
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
DB01752phenylethanolamine N-methyltransferaseexperimentalS-Adenosyl-L-Homocysteine
DB03468phenylethanolamine N-methyltransferaseexperimental1,2,3,4-Tetrahydro-Isoquinoline-7-Sulfonic Acid Amide
DB03824phenylethanolamine N-methyltransferaseexperimental7-Iodo-1,2,3,4-Tetrahydro-Isoquinoline
DB04273phenylethanolamine N-methyltransferaseexperimental8,9-Dichloro-2,3,4,5-Tetrahydro-1h-Benzo[C]Azepine
DB07597phenylethanolamine N-methyltransferaseexperimentalCIS-(1R,2S)-2-AMINO-1,2,3,4-TETRAHYDRONAPHTHALEN-1-OL
DB07739phenylethanolamine N-methyltransferaseexperimental(3R)-3-(FLUOROMETHYL)-7-(THIOMORPHOLIN-4-YLSULFONYL)-1,2,3,4-TETRAHYDROISOQUINOLINE
DB07747phenylethanolamine N-methyltransferaseexperimental(3R)-N-(4-CHLOROPHENYL)-3-(HYDROXYMETHYL)-1,2,3,4-TETRAHYDROISOQUINOLINE-7-SULFONAMIDE
DB07798phenylethanolamine N-methyltransferaseexperimental(3R)-3-(FLUOROMETHYL)-N-(3,3,3-TRIFLUOROPROPYL)-1,2,3,4-TETRAHYDROISOQUINOLINE-7-SULFONAMIDE
DB07906phenylethanolamine N-methyltransferaseexperimental[(3R)-7-NITRO-1,2,3,4-TETRAHYDROISOQUINOLIN-3-YL]METHANOL
DB08128phenylethanolamine N-methyltransferaseexperimental(1S,4R,9S)-5-(trifluoromethyl)-1,2,3,4-tetrahydro-1,4-methanonaphthalen-9-amine
DB08129phenylethanolamine N-methyltransferaseexperimental(1R)-2-amino-1-[3-(trifluoromethyl)phenyl]ethanol
DB08550phenylethanolamine N-methyltransferaseexperimental7,8-DICHLORO-1,2,3,4-TETRAHYDROISOQUINOLINE
DB08631phenylethanolamine N-methyltransferaseexperimentalN-(4-CHLOROPHENYL)-1,2,3,4-TETRAHYDROISOQUINOLINE-7-SULFONAMIDE
DB08654phenylethanolamine N-methyltransferaseexperimentalTRANS-(1S,2S)-2-AMINO-1,2,3,4-TETRAHYDRONAPHTHALEN-1-OL
DB00988phenylethanolamine N-methyltransferaseapprovedDopamine
DB00135phenylethanolamine N-methyltransferaseapproved; nutraceuticalL-Tyrosine
DB00360phenylethanolamine N-methyltransferaseapproved; investigationalTetrahydrobiopterin
DB00126phenylethanolamine N-methyltransferaseapproved; nutraceuticalVitamin C
DB01105phenylethanolamine N-methyltransferaseillicit; approved; withdrawn; investigationalSibutramine
DB00668phenylethanolamine N-methyltransferaseapprovedEpinephrine
DB00368phenylethanolamine N-methyltransferaseapprovedNorepinephrine
DB01454phenylethanolamine N-methyltransferaseillicit; experimental3,4-Methylenedioxymethamphetamine
DB01033phenylethanolamine N-methyltransferaseapprovedMercaptopurine


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Cross referenced IDs for PNMT
* 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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