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 COMT
Basic gene info.Gene symbolCOMT
Gene namecatechol-O-methyltransferase
SynonymsHEL-S-98n
CytomapUCSC genome browser: 22q11.21
Genomic locationchr22 :19939044-19957498
Type of geneprotein-coding
RefGenesNM_000754.3,
NM_001135161.1,NM_001135162.1,NM_007310.2,
Ensembl idENSG00000093010
Descriptioncatechol O-methyltransferaseepididymis secretory sperm binding protein Li 98n
Modification date20141222
dbXrefs MIM : 116790
HGNC : HGNC
Ensembl : ENSG00000093010
HPRD : 00284
Vega : OTTHUMG00000150529
ProteinUniProt: P21964
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_COMT
BioGPS: 1312
Gene Expression Atlas: ENSG00000093010
The Human Protein Atlas: ENSG00000093010
PathwayNCI Pathway Interaction Database: COMT
KEGG: COMT
REACTOME: COMT
ConsensusPathDB
Pathway Commons: COMT
MetabolismMetaCyc: COMT
HUMANCyc: COMT
RegulationEnsembl's Regulation: ENSG00000093010
miRBase: chr22 :19,939,044-19,957,498
TargetScan: NM_000754
cisRED: ENSG00000093010
ContextiHOP: COMT
cancer metabolism search in PubMed: COMT
UCL Cancer Institute: COMT
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of COMT in cancer cell metabolism1. Swift-Scanlan T, Smith CT, Bardowell SA, Boettiger CA (2014) Comprehensive interrogation of CpG island methylation in the gene encoding COMT, a key estrogen and catecholamine regulator. BMC Med Genomics 7: 5. doi: 10.1186/1755-8794-7-5. pmid: 3910242. go to article
2. Yager JD (2015) Mechanisms of estrogen carcinogenesis: The role of E2/E1-quinone metabolites suggests new approaches to preventive intervention - A review. Steroids 99: 56-60. doi: 10.1016/j.steroids.2014.08.006. pmid: 4339663. go to article
3. Hevir-Kene N, Rizner TL (2015) The endometrial cancer cell lines Ishikawa and HEC-1A, and the control cell line HIEEC, differ in expression of estrogen biosynthetic and metabolic genes, and in androstenedione and estrone-sulfate metabolism. Chem Biol Interact 234: 309-319. doi: 10.1016/j.cbi.2014.11.015. go to article

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

check002.gifOthers
OMIM 103780; phenotype.
116790; gene+phenotype.
Orphanet 240863; Cisplatin toxicity.
240999; Susceptibility to deafness due to cisplatin treatment.
3140; Schizophrenia.
567; 22q11.2 deletion syndrome.
DiseaseKEGG Disease: COMT
MedGen: COMT (Human Medical Genetics with Condition)
ClinVar: COMT
PhenotypeMGI: COMT (International Mouse Phenotyping Consortium)
PhenomicDB: COMT

Mutations for COMT
* 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
There's no inter-chromosomal structural variation.
- 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
pancreasCOMTchr221994980419949824TXNRD2chr221992691619926936
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 COMT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CB529248COMT16605221995171419956539NICN160168934946161349461701
BG259212IQSEC132734631294251612942535COMT334357221994648119946506
BI053757COMT2487221995631419956377MAP7D18145713664486336645663
AI360037COMT1356221995742019957775PCBP2350465125384914053849736
BI053724COMT1274221995631419956377MAP7D16844413664486336645663
AW340773COMT5340221995716819957503THBS33374261155177604155177693
AI298713COMT971221995122219951284COMT67497221995170219956367

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=7)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr22:19951207-19951207p.L136L3
chr22:19950268-19950268p.Q73Q2
chr22:19951164-19951164p.S122L2
chr22:19950093-19950093p.G15V2
chr22:19950221-19950221p.R58C2
chr22:19951785-19951785p.W193*1
chr22:19950294-19950294p.Y82C1
chr22:19951793-19951793p.R196W1
chr22:19950334-19950334p.K95N1
chr22:19956054-19956054p.?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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample4     1 1    1  36 2
# mutation4     1 1    1  36 2
nonsynonymous SNV2               25 2
synonymous SNV2     1 1    1  11  
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
chr22:19951251p.R146W,COMT1
chr22:19956195p.L148M,COMT1
chr22:19951738p.G163R,COMT1
chr22:19951777p.P174P,COMT1
chr22:19951781p.H182H,COMT1
chr22:19951793p.R184C,COMT1
chr22:19950226p.I9I,COMT1
chr22:19951799p.H193Y,COMT1
chr22:19950294p.Y32C,COMT1
chr22:19956080p.R201M,COMT1

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 COMT 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 COMT

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,LRRC75B,COMT,DDT,DGCR14,DGCR6,DGCR6L,
GCAT,MCAT,MRPL41,NOL12,RHBDD3,RPS19BP1,SGSM3,
THAP7,TRMT2A,TXN2,TXNRD2,UBE2L3,UFD1L,UQCR10
EMC10,CHPF,COASY,COMT,CORO1B,DDX41,DUS1L,
LMAN2,LRRC45,LYPLA2,NARFL,NDOR1,NMRAL1,PIGQ,
PUSL1,RABEP2,RANGAP1,RPUSD1,TMEM141,TRAPPC6A,YIPF2

ADSL,ARL2,BID,COMT,DRG1,MIF,MPST,
MRPL40,NHP2L1,NIPSNAP1,PLA2G12B,POLR2F,RPS19BP1,SLC25A1,
SLC39A5,SNRPD3,THAP7,TRMT2A,UQCR10,YDJC,ZMAT5
ABHD14A,C12orf10,CHID1,COMT,CREG1,CUEDC2,DRG2,
EIF3G,ELP2,MRPL9,NINJ1,PEMT,RBMX2,RNF130,
RPUSD4,RSL1D1,SIGMAR1,ST7,TMEM147,TMEM150A,ZC3HC1
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 COMT
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P21964; -.
ChemistryChEMBL CHEMBL2023; -.
ChemistryGuidetoPHARMACOLOGY 2472; -.
Organism-specific databasesPharmGKB PA117; -.
Organism-specific databasesCTD 1312; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00118catechol-O-methyltransferaseapproved; nutraceuticalS-Adenosylmethionine
DB00323catechol-O-methyltransferaseapproved; withdrawnTolcapone
DB00494catechol-O-methyltransferaseapproved; investigationalEntacapone
DB02105catechol-O-methyltransferaseexperimental3,5-Dinitrocatechol
DB03336catechol-O-methyltransferaseexperimentalBIA
DB03907catechol-O-methyltransferaseexperimentalN-{3-[5-(6-Amino-Purin-9-Yl)-3,4-Dihydroxy-Tetrahydro-Furan-2-Yl]-Allyl}-2,3-Dihydroxy-5-Nitro-Benzamide
DB04820catechol-O-methyltransferasewithdrawnNialamide
DB07462catechol-O-methyltransferaseexperimental(3,4-DIHYDROXY-2-NITROPHENYL)(PHENYL)METHANONE
DB08049catechol-O-methyltransferaseexperimental7,8-dihydroxy-4-phenyl-2H-chromen-2-one
DB00286catechol-O-methyltransferaseapprovedConjugated Estrogens
DB00571catechol-O-methyltransferaseapproved; investigationalPropranolol
DB00215catechol-O-methyltransferaseapprovedCitalopram
DB00472catechol-O-methyltransferaseapprovedFluoxetine
DB00988catechol-O-methyltransferaseapprovedDopamine
DB00318catechol-O-methyltransferaseillicit; approvedCodeine
DB00907catechol-O-methyltransferaseillicit; approvedCocaine
DB00476catechol-O-methyltransferaseapprovedDuloxetine
DB00864catechol-O-methyltransferaseapproved; investigationalTacrolimus
DB00640catechol-O-methyltransferaseapproved; investigationalAdenosine
DB00134catechol-O-methyltransferaseapproved; nutraceuticalL-Methionine
DB01156catechol-O-methyltransferaseapprovedBupropion
DB00334catechol-O-methyltransferaseapproved; investigationalOlanzapine
DB01452catechol-O-methyltransferaseillicit; experimentalHeroin
DB00734catechol-O-methyltransferaseapproved; investigationalRisperidone
DB00295catechol-O-methyltransferaseapproved; investigationalMorphine
DB00745catechol-O-methyltransferaseapproved; investigationalModafinil
DB00115catechol-O-methyltransferaseapproved; nutraceuticalCyanocobalamin
DB00158catechol-O-methyltransferaseapproved; nutraceuticalFolic Acid
DB01454catechol-O-methyltransferaseillicit; experimental3,4-Methylenedioxymethamphetamine
DB01235catechol-O-methyltransferaseapprovedLevodopa
DB00668catechol-O-methyltransferaseapprovedEpinephrine
DB01033catechol-O-methyltransferaseapprovedMercaptopurine
DB00945catechol-O-methyltransferaseapprovedAcetylsalicylic acid
DB00968catechol-O-methyltransferaseapprovedMethyldopa
DB00184catechol-O-methyltransferaseapprovedNicotine
DB00515catechol-O-methyltransferaseapprovedCisplatin
DB00422catechol-O-methyltransferaseapproved; investigationalMethylphenidate


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Cross referenced IDs for COMT
* 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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