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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for DNMT3A |
Basic gene info. | Gene symbol | DNMT3A |
Gene name | DNA (cytosine-5-)-methyltransferase 3 alpha | |
Synonyms | DNMT3A2|M.HsaIIIA|TBRS | |
Cytomap | UCSC genome browser: 2p23 | |
Genomic location | chr2 :25455829-25565459 | |
Type of gene | protein-coding | |
RefGenes | NM_022552.4, NM_153759.3,NM_175629.2,NM_175630.1, | |
Ensembl id | ENSG00000119772 | |
Description | DNA (cytosine-5)-methyltransferase 3ADNA MTase HsaIIIADNA cytosine methyltransferase 3A2 | |
Modification date | 20141207 | |
dbXrefs | MIM : 602769 | |
HGNC : HGNC | ||
Ensembl : ENSG00000119772 | ||
HPRD : 04141 | ||
Vega : OTTHUMG00000094777 | ||
Protein | UniProt: Q9Y6K1 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_DNMT3A | |
BioGPS: 1788 | ||
Gene Expression Atlas: ENSG00000119772 | ||
The Human Protein Atlas: ENSG00000119772 | ||
Pathway | NCI Pathway Interaction Database: DNMT3A | |
KEGG: DNMT3A | ||
REACTOME: DNMT3A | ||
ConsensusPathDB | ||
Pathway Commons: DNMT3A | ||
Metabolism | MetaCyc: DNMT3A | |
HUMANCyc: DNMT3A | ||
Regulation | Ensembl's Regulation: ENSG00000119772 | |
miRBase: chr2 :25,455,829-25,565,459 | ||
TargetScan: NM_022552 | ||
cisRED: ENSG00000119772 | ||
Context | iHOP: DNMT3A | |
cancer metabolism search in PubMed: DNMT3A | ||
UCL Cancer Institute: DNMT3A | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of DNMT3A in cancer cell metabolism | 1. 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) |
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Cancer | CGAP: DNMT3A |
Familial Cancer Database: DNMT3A |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in LAML 6, |
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/ |
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KEGG_CYSTEINE_AND_METHIONINE_METABOLISM |
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OMIM | 602769; gene. 615879; phenotype. |
Orphanet | 404443; Tall stature-intellectual disability-facial dysmorphism syndrome. |
Disease | KEGG Disease: DNMT3A |
MedGen: DNMT3A (Human Medical Genetics with Condition) | |
ClinVar: DNMT3A | |
Phenotype | MGI: 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. |
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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | DNMT3A | chr2 | 25461431 | 25461451 | chr12 | 71469636 | 71469656 | |
ovary | DNMT3A | chr2 | 25486052 | 25486072 | ADCY3 | chr2 | 25132237 | 25132257 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DNMT3A related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BF083029 | DNMT3A | 1 | 144 | 2 | 25494257 | 25494403 | NUMA1 | 137 | 387 | 11 | 71714303 | 71714553 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
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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Stat. for Non-Synonymous SNVs (# total SNVs=1398) | (# total SNVs=32) |
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(# total SNVs=94) | (# total SNVs=22) |
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* 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 position | Mutation(aa) | Unique sampleID count |
chr2:25457242-25457242 | p.R882H | 432 |
chr2:25457243-25457243 | p.R882S | 187 |
chr2:25463541-25463541 | p.S714C | 11 |
chr2:25467449-25467449 | p.G543C | 10 |
chr2:25466800-25466800 | p.R635W | 9 |
chr2:25457176-25457176 | p.P904L | 7 |
chr2:25463300-25463302 | p.F731del | 7 |
chr2:25463184-25463184 | p.S770L | 7 |
chr2:25463181-25463181 | p.R771Q | 6 |
chr2:25462032-25462032 | p.R792H | 5 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 | 4 | 1 | 21 |   |   | 11 |   | 5 | 1 | 41 | 14 | 9 | 5 |   | 2 | 7 | 12 | 1 | 11 |
# mutation | 1 | 4 | 1 | 23 |   |   | 11 |   | 5 | 1 | 15 | 17 | 9 | 5 |   | 2 | 7 | 13 | 1 | 12 |
nonsynonymous SNV | 1 | 4 | 1 | 17 |   |   | 7 |   | 5 | 1 | 15 | 15 | 6 | 4 |   |   | 4 | 10 | 1 | 8 |
synonymous SNV |   |   |   | 6 |   |   | 4 |   |   |   |   | 2 | 3 | 1 |   | 2 | 3 | 3 |   | 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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* 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 Position | Mutation(aa) | Unique sampleID count |
chr2:25457242 | p.R693H,DNMT3A | 23 |
chr2:25457243 | p.R693C,DNMT3A | 7 |
chr2:25463307 | p.R540Q,DNMT3A | 2 |
chr2:25463308 | p.R540W,DNMT3A | 2 |
chr2:25463181 | p.A721V,DNMT3A | 2 |
chr2:25457158 | p.A721S,DNMT3A | 2 |
chr2:25457159 | p.R603H,DNMT3A | 2 |
chr2:25463523 | p.R531P,DNMT3A | 2 |
chr2:25469528 | p.F720C,DNMT3A | 2 |
chr2:25523110 | p.R470H,DNMT3A | 2 |
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* 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. |
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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 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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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 |
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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 |
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* 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 |
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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 |
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