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 DNMT3A
Basic gene info.Gene symbolDNMT3A
Gene nameDNA (cytosine-5-)-methyltransferase 3 alpha
SynonymsDNMT3A2|M.HsaIIIA|TBRS
CytomapUCSC genome browser: 2p23
Genomic locationchr2 :25455829-25565459
Type of geneprotein-coding
RefGenesNM_022552.4,
NM_153759.3,NM_175629.2,NM_175630.1,
Ensembl idENSG00000119772
DescriptionDNA (cytosine-5)-methyltransferase 3ADNA MTase HsaIIIADNA cytosine methyltransferase 3A2
Modification date20141207
dbXrefs MIM : 602769
HGNC : HGNC
Ensembl : ENSG00000119772
HPRD : 04141
Vega : OTTHUMG00000094777
ProteinUniProt: Q9Y6K1
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DNMT3A
BioGPS: 1788
Gene Expression Atlas: ENSG00000119772
The Human Protein Atlas: ENSG00000119772
PathwayNCI Pathway Interaction Database: DNMT3A
KEGG: DNMT3A
REACTOME: DNMT3A
ConsensusPathDB
Pathway Commons: DNMT3A
MetabolismMetaCyc: DNMT3A
HUMANCyc: DNMT3A
RegulationEnsembl's Regulation: ENSG00000119772
miRBase: chr2 :25,455,829-25,565,459
TargetScan: NM_022552
cisRED: ENSG00000119772
ContextiHOP: DNMT3A
cancer metabolism search in PubMed: DNMT3A
UCL Cancer Institute: DNMT3A
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DNMT3A in cancer cell metabolism1. Holmberg Olausson K, Nister M, Lindstrom MS (2014) Loss of nucleolar histone chaperone NPM1 triggers rearrangement of heterochromatin and synergizes with a deficiency in DNA methyltransferase DNMT3A to drive ribosomal DNA transcription. J Biol Chem 289: 34601-34619. doi: 10.1074/jbc.M114.569244. pmid: 4263867. go to article
2. Arechederra M, Priego N, Vazquez-Carballo A, Sequera C, Gutierrez-Uzquiza A, et al. (2015) p38 MAPK down-regulates fibulin 3 expression through methylation of gene regulatory sequences: role in migration and invasion. J Biol Chem 290: 4383-4397. doi: 10.1074/jbc.M114.582239. pmid: 4326844. go to article

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Phenotypic Information for DNMT3A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DNMT3A
Familial Cancer Database: DNMT3A
* 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 LAML 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.nejm.org/doi/full/10.1056/NEJMoa1301689,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM

check002.gifOthers
OMIM 602769; gene.
615879; phenotype.
Orphanet 404443; Tall stature-intellectual disability-facial dysmorphism syndrome.
DiseaseKEGG Disease: DNMT3A
MedGen: DNMT3A (Human Medical Genetics with Condition)
ClinVar: DNMT3A
PhenotypeMGI: DNMT3A (International Mouse Phenotyping Consortium)
PhenomicDB: DNMT3A

Mutations for DNMT3A
* 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
ovaryDNMT3Achr22546143125461451chr127146963671469656
ovaryDNMT3Achr22548605225486072ADCY3chr22513223725132257
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 DNMT3A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF083029DNMT3A114422549425725494403NUMA1137387117171430371714553

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=904

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=1398)
Stat. for Synonymous SNVs
(# total SNVs=32)
Stat. for Deletions
(# total SNVs=94)
Stat. for Insertions
(# total SNVs=22)

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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
chr2:25457242-25457242p.R882H432
chr2:25457243-25457243p.R882S187
chr2:25463541-25463541p.S714C11
chr2:25467449-25467449p.G543C10
chr2:25466800-25466800p.R635W9
chr2:25457176-25457176p.P904L7
chr2:25463184-25463184p.S770L7
chr2:25463300-25463302p.F731del7
chr2:25463181-25463181p.R771Q6
chr2:25467134-25467134p.W581R5

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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=22

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample14121  11 51411495 2712111
# mutation14123  11 51151795 2713112
nonsynonymous SNV14117  7 51151564  41018
synonymous SNV   6  4    231 233 4
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
chr2:25457242p.R693H,DNMT3A23
chr2:25457243p.R693C,DNMT3A7
chr2:25463308p.R540Q,DNMT3A2
chr2:25463181p.R540W,DNMT3A2
chr2:25457158p.A721V,DNMT3A2
chr2:25457159p.A721S,DNMT3A2
chr2:25463523p.R603H,DNMT3A2
chr2:25469528p.R531P,DNMT3A2
chr2:25523110p.F720C,DNMT3A2
chr2:25457161p.R470H,DNMT3A2

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 DNMT3A 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 DNMT3A

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

CAD,CBX2,CENPA,CENPO,CPSF3,DNMT3A,FAM136A,
FAM64A,GPC2,GTF3C2,KDM2B,KIF3C,MEX3A,OTX1,
PPM1G,RCC2,STMN1,TET3,TUBB,YEATS2,YWHAQ
AHDC1,ANKRD52,C15orf52,DAG1,DNMT3A,EXTL1,FOXK2,
GPR157,GTF3C1,JARID2,MYO18A,OIP5,PADI2,PDCD11,
POLR3D,RCOR2,SBK1,SEMA4D,UBE2O,UBQLN4,ZNF710

ACVR2B,AMMECR1L,ATAD2B,BCL9,CBFA2T2,CHD6,CLASP1,
DHX57,DNMT3A,EPC2,JARID2,GSE1,KIDINS220,LDB1,
MEX3A,NOTCH1,PBX2,PMFBP1,TET3,TP53BP1,ZSCAN2
ASXL1,ATF7,ATXN2,BCL9,BCORL1,BRD3,CHD6,
DNMT3A,ERCC4,HDAC7,NCKAP5L,PHF12,RAI1,REV3L,
SEPN1,SIX5,TBC1D24,TRERF1,ZMYM3,ZNF444,ZNF618
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 DNMT3A


There's no related Drug.
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Cross referenced IDs for DNMT3A
* 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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