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 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)

Cancer 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/

Metabolic Pathway Description
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM

Others
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)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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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'.

- 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'.

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DNMT3A related fusion information.

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

144

25494257

25494403

NUMA1

137

387

71714303

71714553

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=904

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Somatic 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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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
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
chr2:25463184-25463184	p.S770L	7
chr2:25463300-25463302	p.F731del	7
chr2:25463181-25463181	p.R771Q	6
chr2:25467134-25467134	p.W581R	5

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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=22

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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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
chr2:25457242	p.R693H,DNMT3A	23
chr2:25457243	p.R693C,DNMT3A	7
chr2:25463308	p.R540Q,DNMT3A	2
chr2:25463181	p.R540W,DNMT3A	2
chr2:25457158	p.A721V,DNMT3A	2
chr2:25457159	p.A721S,DNMT3A	2
chr2:25463523	p.R603H,DNMT3A	2
chr2:25469528	p.R531P,DNMT3A	2
chr2:25523110	p.F720C,DNMT3A	2
chr2:25457161	p.R470H,DNMT3A	2

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 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

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


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

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 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