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 DNMT3B
Basic gene info.Gene symbolDNMT3B
Gene nameDNA (cytosine-5-)-methyltransferase 3 beta
SynonymsICF|ICF1|M.HsaIIIB
CytomapUCSC genome browser: 20q11.2
Genomic locationchr20 :31350190-31397162
Type of geneprotein-coding
RefGenesNM_001207055.1,
NM_001207056.1,NM_006892.3,NM_175848.1,NM_175849.1,
NM_175850.2,
Ensembl idENSG00000088305
DescriptionDNA (cytosine-5)-methyltransferase 3BDNA MTase HsaIIIBDNA methyltransferase HsaIIIB
Modification date20141221
dbXrefs MIM : 602900
HGNC : HGNC
Ensembl : ENSG00000088305
HPRD : 04209
Vega : OTTHUMG00000032226
ProteinUniProt: Q9UBC3
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DNMT3B
BioGPS: 1789
Gene Expression Atlas: ENSG00000088305
The Human Protein Atlas: ENSG00000088305
PathwayNCI Pathway Interaction Database: DNMT3B
KEGG: DNMT3B
REACTOME: DNMT3B
ConsensusPathDB
Pathway Commons: DNMT3B
MetabolismMetaCyc: DNMT3B
HUMANCyc: DNMT3B
RegulationEnsembl's Regulation: ENSG00000088305
miRBase: chr20 :31,350,190-31,397,162
TargetScan: NM_001207055
cisRED: ENSG00000088305
ContextiHOP: DNMT3B
cancer metabolism search in PubMed: DNMT3B
UCL Cancer Institute: DNMT3B
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DNMT3B in cancer cell metabolism1. Sin-Chan P, Huang A (2014) DNMTs as potential therapeutic targets in high-risk pediatric embryonal brain tumors. Expert Opin Ther Targets 18: 1103-1107. doi: 10.1517/14728222.2014.938052. 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

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Phenotypic Information for DNMT3B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DNMT3B
Familial Cancer Database: DNMT3B
* 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_CYSTEINE_AND_METHIONINE_METABOLISM

check002.gifOthers
OMIM 242860; phenotype.
242860; phenotype.
602900; gene.
602900; gene.
Orphanet 2268; ICF syndrome.
2268; ICF syndrome.
DiseaseKEGG Disease: DNMT3B
MedGen: DNMT3B (Human Medical Genetics with Condition)
ClinVar: DNMT3B
PhenotypeMGI: DNMT3B (International Mouse Phenotyping Consortium)
PhenomicDB: DNMT3B

Mutations for DNMT3B
* 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 DNMT3B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB451208FUK1409167048832870497624DNMT3B407477203139024031390310
AW794433DNMT3B1142203139647531396615SYK13121099365796893658047

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 # sample1     2 1        
GAIN (# sample)      2 1        
LOSS (# sample)1                
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=83)
Stat. for Synonymous SNVs
(# total SNVs=35)
Stat. for Deletions
(# total SNVs=3)
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
chr20:31386384-31386384p.R537W3
chr20:31386409-31386409p.R545H3
chr20:31372633-31372633p.R92W2
chr20:31375143-31375143p.T180T2
chr20:31386449-31386449p.Y558Y2
chr20:31368225-31368225p.S32S2
chr20:31386378-31386378p.V535I2
chr20:31389107-31389107p.E674K2
chr20:31394046-31394046p.S778L2
chr20:31388003-31388003p.V602I2

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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
# sample13 222 6 221953  1113 12
# mutation13 232 6 2211153  1015 16
nonsynonymous SNV12 141 5 111742  67 10
synonymous SNV 1 91 1 11 411  48 6
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
chr20:31372633p.V153V,DNMT3B2
chr20:31394046p.R122G,DNMT3B2
chr20:31368260p.P44L,DNMT3B2
chr20:31375143p.S758L,DNMT3B2
chr20:31375164p.T104T,DNMT3B2
chr20:31386384p.P111P,DNMT3B2
chr20:31374365p.R441W,DNMT3B2
chr20:31386409p.R92W,DNMT3B2
chr20:31376692p.R449H,DNMT3B2
chr20:31372593p.R681Q,DNMT3B1

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 DNMT3B 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 DNMT3B

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

AURKB,CBX2,CENPA,DNMT3B,ERCC6L,FAM171A2,GINS1,
KIF20A,KIF4A,MELK,MEX3A,MYBL2,NCAPH,ORC6,
PDSS1,SOX11,SUV39H2,TPX2,TUBB,UBE2T,ZNF695
DNMT3B,EZH2,FANCD2,HELLS,KDM5B,KIAA1549,KIF24,
MYO19,NAA40,NBEAL2,PGBD2,PHF12,PLCH1,PLEKHG4B,
PRDM15,SLC12A8,STIL,TET3,VANGL2,ZMYM3,ZFP69B

ACTR5,ASXL1,GID8,CDK5RAP1,CEP250,CSE1L,CSTF1,
DDX27,DHX35,DNMT3B,TTI1,LSM14B,MAPRE1,MOCS3,
NFS1,SS18L1,TAF4,NELFCD,TPX2,TTPAL,YTHDF1
KIAA1456,DCP2,DNMT3B,FGF11,FKTN,FNBP1L,KREMEN1,
LIMD1,MDM2,MTSS1,PHF14,PLAGL1,PPM1H,PVRL1,
RASA1,RPS6KA6,STX6,TAF5,TBC1D4,USP46,ZBTB10
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 DNMT3B


There's no related Drug.
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Cross referenced IDs for DNMT3B
* 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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