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 DNMT1

Basic gene info.	Gene symbol	DNMT1
	Gene name	DNA (cytosine-5-)-methyltransferase 1
	Synonyms	ADCADN\|AIM\|CXXC9\|DNMT\|HSN1E\|MCMT
	Cytomap	UCSC genome browser: 19p13.2
	Genomic location	chr19 :10244021-10305755
	Type of gene	protein-coding
	RefGenes	NM_001130823.1, NM_001379.2,
	Ensembl id	ENSG00000130816
	Description	CXXC-type zinc finger protein 9DNA (cytosine-5)-methyltransferase 1DNA MTase HsaIDNA methyltransferase HsaIm.HsaI
	Modification date	20141222
dbXrefs	MIM : 126375
	HGNC : HGNC
	Ensembl : ENSG00000130816
	HPRD : 00532
	Vega : OTTHUMG00000180397
Protein	UniProt: P26358 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DNMT1
	BioGPS: 1786
	Gene Expression Atlas: ENSG00000130816
	The Human Protein Atlas: ENSG00000130816
Pathway	NCI Pathway Interaction Database: DNMT1
	KEGG: DNMT1
	REACTOME: DNMT1
	ConsensusPathDB
	Pathway Commons: DNMT1
Metabolism	MetaCyc: DNMT1
	HUMANCyc: DNMT1
Regulation	Ensembl's Regulation: ENSG00000130816
	miRBase: chr19 :10,244,021-10,305,755
	TargetScan: NM_001130823
	cisRED: ENSG00000130816
Context	iHOP: DNMT1
	cancer metabolism search in PubMed: DNMT1
	UCL Cancer Institute: DNMT1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DNMT1 in cancer cell metabolism	1. Oh HR, An CH, Yoo NJ, Lee SH (2014) Somatic mutations of amino acid metabolism-related genes in gastric and colorectal cancers and their regional heterogeneity--a short report. Cell Oncol (Dordr) 37: 455-461. doi: 10.1007/s13402-014-0209-1. 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 3. Fang YY, Bi FF, Zhou YM, Sun WP, Li CY, et al. (2015) Nicotinamide adenine dinucleotide (NAD) may affect DNA methyltransferase 1 through regulation of BRCA1 in ovarian cancer. Am J Cancer Res 5: 1199-1206. pmid: 4449447. go to article 4. Karlic H, Thaler R, Gerner C, Grunt T, Proestling K, et al. (2015) Inhibition of the mevalonate pathway affects epigenetic regulation in cancer cells. Cancer Genet 208: 241-252. doi: 10.1016/j.cancergen.2015.03.008. go to article

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Phenotypic Information for DNMT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: DNMT1
	Familial Cancer Database: DNMT1

* 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	126375; gene. 604121; phenotype. 614116; phenotype.
Orphanet	314404; Autosomal dominant cerebellar ataxia, deafness and narcolepsy.
Disease	KEGG Disease: DNMT1
	MedGen: DNMT1 (Human Medical Genetics with Condition)
	ClinVar: DNMT1
Phenotype	MGI: DNMT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DNMT1

Mutations for DNMT1

* 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

There's no inter-chromosomal structural variation.

- 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
pancreas	DNMT1	chr19	10291529	10291549		chr19	21523865	21523885

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 DNMT1 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

AI810847

DNMT1

213

10244022

10244223

MALAT1

212

287

65268124

65268199

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=107)	Stat. for Synonymous SNVs (# total SNVs=39)

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
chr19:10267124-10267124	p.E432K	5
chr19:10254637-10254637	p.R958H	4
chr19:10291528-10291528	p.E51K	3
chr19:10248608-10248608	p.S1382L	3
chr19:10262139-10262139	p.M718fs*59	3
chr19:10249138-10249138	p.K1348K	3
chr19:10249143-10249143	p.D1347N	3
chr19:10265386-10265386	p.A554T	2
chr19:10265043-10265043	p.A633T	2
chr19:10291054-10291054	p.R139S	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=3

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	5	6	1	30	2		6		7		1	7	4	2		3	15	16	1	17
# mutation	6	6	1	30	2		6		7		1	7	4	2		3	21	18	1	20
nonsynonymous SNV	4	3	1	21			4		7		1	5	4	2		3	15	14	1	13
synonymous SNV	2	3		9	2		2					2					6	4		7

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
chr19:10277310	p.E432K,DNMT1	3
chr19:10267124	p.G269G,DNMT1	3
chr19:10291528	p.E51K,DNMT1	3
chr19:10246814	p.E1531Q,DNMT1	2
chr19:10249209	p.A554P,DNMT1	2
chr19:10265386	p.P1325S,DNMT1	2
chr19:10250386	p.R1289H,DNMT1	2
chr19:10257086	p.N929N,DNMT1	2
chr19:10265724	p.E485K,DNMT1	2
chr19:10273416	p.D859N,DNMT1	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 DNMT1 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 DNMT1

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


CDCA7,CDK2,CHAF1A,CHEK1,CLSPN,DNMT1,ILF3, INCENP,KHSRP,KIF18B,KIF4A,MCM2,MCM3,MCM6, MSH2,MSH6,NCAPH,ORC1,SMARCA4,SPC24,UHRF1	CABIN1,CAD,CHD3,CHD4,DNMT1,HYOU1,ILF3, KDM5C,MARK2,MOV10,MYO19,NBEAL2,NUP210,PCNXL3, PDCD11,PLXNB2,RAI1,SIPA1L3,SMARCA4,TCF3,VAV2

BRIP1,TICRR,CDCA5,CHAF1A,CLSPN,DNMT1,EXO1, GSG2,HNRNPM,ILF3,INCENP,KIF18B,LMNB2,MCM2, MKI67,NCAPD3,NCAPH,ORC1,UHRF1,WDHD1,WDR62	ATAD2,BLM,BRCA1,CLSPN,DNMT1,FANCA,LMNB2, MCM2,MCM3,MCM5,NCAPD3,NCAPG2,NUP188,ODF2, PFAS,RBM14,TACC3,TIMELESS,UHRF1,WDHD1,WDR62

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 DNMT1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P26358; -.
Chemistry	ChEMBL	CHEMBL1993; -.
Organism-specific databases	PharmGKB	PA27443; -.
Organism-specific databases	CTD	1786; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00928	DNA (cytosine-5-)-methyltransferase 1	approved; investigational	Azacitidine
DB01035	DNA (cytosine-5-)-methyltransferase 1	approved	Procainamide
DB01099	DNA (cytosine-5-)-methyltransferase 1	approved	Flucytosine
DB01262	DNA (cytosine-5-)-methyltransferase 1	approved; investigational	Decitabine

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Cross referenced IDs for DNMT1

* 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