Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	DNMT3B
	Gene name	DNA (cytosine-5-)-methyltransferase 3 beta
	Synonyms	ICF\|ICF1\|M.HsaIIIB
	Cytomap	UCSC genome browser: 20q11.2
	Genomic location	chr20 :31350190-31397162
	Type of gene	protein-coding
	RefGenes	NM_001207055.1, NM_001207056.1,NM_006892.3,NM_175848.1,NM_175849.1, NM_175850.2,
	Ensembl id	ENSG00000088305
	Description	DNA (cytosine-5)-methyltransferase 3BDNA MTase HsaIIIBDNA methyltransferase HsaIIIB
	Modification date	20141221
dbXrefs	MIM : 602900
	HGNC : HGNC
	Ensembl : ENSG00000088305
	HPRD : 04209
	Vega : OTTHUMG00000032226
Protein	UniProt: Q9UBC3 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DNMT3B
	BioGPS: 1789
	Gene Expression Atlas: ENSG00000088305
	The Human Protein Atlas: ENSG00000088305
Pathway	NCI Pathway Interaction Database: DNMT3B
	KEGG: DNMT3B
	REACTOME: DNMT3B
	ConsensusPathDB
	Pathway Commons: DNMT3B
Metabolism	MetaCyc: DNMT3B
	HUMANCyc: DNMT3B
Regulation	Ensembl's Regulation: ENSG00000088305
	miRBase: chr20 :31,350,190-31,397,162
	TargetScan: NM_001207055
	cisRED: ENSG00000088305
Context	iHOP: DNMT3B
	cancer metabolism search in PubMed: DNMT3B
	UCL Cancer Institute: DNMT3B
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DNMT3B in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM

Others
OMIM	242860; phenotype. 242860; phenotype. 602900; gene. 602900; gene.
Orphanet	2268; ICF syndrome. 2268; ICF syndrome.
Disease	KEGG Disease: DNMT3B
	MedGen: DNMT3B (Human Medical Genetics with Condition)
	ClinVar: DNMT3B
Phenotype	MGI: DNMT3B (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DNMT3B 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
DB451208	FUK	1	409	16	70488328	70497624	DNMT3B	407	477	20	31390240	31390310
AW794433	DNMT3B	1	142	20	31396475	31396615	SYK	131	210	9	93657968	93658047

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr20:31386409-31386409	p.R545H	3
chr20:31386384-31386384	p.R537W	3
chr20:31388003-31388003	p.V602I	2
chr20:31394046-31394046	p.S778L	2
chr20:31389138-31389138	p.P684L	2
chr20:31383226-31383226	p.R380*	2
chr20:31387093-31387093	p.R573L	2
chr20:31379488-31379488	p.R299*	2
chr20:31375119-31375119	p.D172D	2
chr20:31383271-31383271	p.A395T	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	3		22	2		6		2	2	1	9	5	3			11	13		12
# mutation	1	3		23	2		6		2	2	1	11	5	3			10	15		16
nonsynonymous SNV	1	2		14	1		5		1	1	1	7	4	2			6	7		10
synonymous SNV		1		9	1		1		1	1		4	1	1			4	8		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr20:31375143	p.S758L,DNMT3B	2
chr20:31375164	p.T104T,DNMT3B	2
chr20:31386384	p.P111P,DNMT3B	2
chr20:31374365	p.R441W,DNMT3B	2
chr20:31386409	p.R92W,DNMT3B	2
chr20:31376692	p.R449H,DNMT3B	2
chr20:31372633	p.V153V,DNMT3B	2
chr20:31394046	p.R122G,DNMT3B	2
chr20:31368260	p.P44L,DNMT3B	2
chr20:31386361	p.K747N,DNMT3B	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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