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 DNMT1
Basic gene info.Gene symbolDNMT1
Gene nameDNA (cytosine-5-)-methyltransferase 1
CytomapUCSC genome browser: 19p13.2
Genomic locationchr19 :10244021-10305755
Type of geneprotein-coding
Ensembl idENSG00000130816
DescriptionCXXC-type zinc finger protein 9DNA (cytosine-5)-methyltransferase 1DNA MTase HsaIDNA methyltransferase HsaIm.HsaI
Modification date20141222
dbXrefs MIM : 126375
Ensembl : ENSG00000130816
HPRD : 00532
Vega : OTTHUMG00000180397
ProteinUniProt: P26358
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DNMT1
BioGPS: 1786
Gene Expression Atlas: ENSG00000130816
The Human Protein Atlas: ENSG00000130816
PathwayNCI Pathway Interaction Database: DNMT1
Pathway Commons: DNMT1
MetabolismMetaCyc: DNMT1
RegulationEnsembl's Regulation: ENSG00000130816
miRBase: chr19 :10,244,021-10,305,755
TargetScan: NM_001130823
cisRED: ENSG00000130816
ContextiHOP: DNMT1
cancer metabolism search in PubMed: DNMT1
UCL Cancer Institute: DNMT1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DNMT1 in cancer cell metabolism1. Oh HR, An CH, Yoo NJ, Lee SH (2014) Somatic mutations of amino acid metabolism-related genes in gastric and colorectal cancers and their regional heterogeneity--a short report. Cell Oncol (Dordr) 37: 455-461. doi: 10.1007/s13402-014-0209-1. go to article
2. Cheng TD, Makar KW, Neuhouser ML, Miller JW, Song X, et al. (2015) Folate-mediated one-carbon metabolism genes and interactions with nutritional factors on colorectal cancer risk: Women's Health Initiative Observational Study. Cancer. doi: 10.1002/cncr.29465. go to article
3. Fang YY, Bi FF, Zhou YM, Sun WP, Li CY, et al. (2015) Nicotinamide adenine dinucleotide (NAD) may affect DNA methyltransferase 1 through regulation of BRCA1 in ovarian cancer. Am J Cancer Res 5: 1199-1206. pmid: 4449447. go to article
4. Karlic H, Thaler R, Gerner C, Grunt T, Proestling K, et al. (2015) Inhibition of the mevalonate pathway affects epigenetic regulation in cancer cells. Cancer Genet 208: 241-252. doi: 10.1016/j.cancergen.2015.03.008. go to article

Phenotypic Information for DNMT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DNMT1
Familial Cancer Database: DNMT1
* 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;,
2 Tumor Suppressor gene;,
3 Cancer Gene Census;,
4 CancerGenes;,
5 Network of Cancer Gene;,
1Therapeutic Vulnerabilities in Cancer;

check002.gifMetabolic Pathway Description

OMIM 126375; gene.
604121; phenotype.
614116; phenotype.
Orphanet 314404; Autosomal dominant cerebellar ataxia, deafness and narcolepsy.
DiseaseKEGG Disease: DNMT1
MedGen: DNMT1 (Human Medical Genetics with Condition)
ClinVar: DNMT1
PhenotypeMGI: DNMT1 (International Mouse Phenotyping Consortium)
PhenomicDB: DNMT1

Mutations for DNMT1
* 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'.
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 DNMT1 related fusion information.
IDHead GeneTail Gene

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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)

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

check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=107)
Stat. for Synonymous SNVs
(# total SNVs=39)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

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

check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample561302 6 7 1742 31516117
# mutation661302 6 7 1742 32118120
nonsynonymous SNV43121  4 7 1542 31514113
synonymous SNV23 92 2    2    64 7
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])

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

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 DNMT1 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]

Gene Expression for DNMT1

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))
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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


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

check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Pharmacological Information for DNMT1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P26358; -.
ChemistryChEMBL CHEMBL1993; -.
Organism-specific databasesPharmGKB PA27443; -.
Organism-specific databasesCTD 1786; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00928DNA (cytosine-5-)-methyltransferase 1approved; investigationalAzacitidine
DB01035DNA (cytosine-5-)-methyltransferase 1approvedProcainamide
DB01099DNA (cytosine-5-)-methyltransferase 1approvedFlucytosine
DB01262DNA (cytosine-5-)-methyltransferase 1approved; investigationalDecitabine

Cross referenced IDs for DNMT1
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories.

: Open all cross reference information

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