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 ENTPD1

Basic gene info.	Gene symbol	ENTPD1
	Gene name	ectonucleoside triphosphate diphosphohydrolase 1
	Synonyms	ATPDase\|CD39\|NTPDase-1\|SPG64
	Cytomap	UCSC genome browser: 10q24
	Genomic location	chr10 :97515672-97637023
	Type of gene	protein-coding
	RefGenes	NM_001098175.1, NM_001164178.1,NM_001164179.1,NM_001164181.1,NM_001164182.1, NM_001164183.1,NM_001776.5,
	Ensembl id	ENSG00000138185
	Description	CD39 antigenNTPDase 1ecto-ATP diphosphohydrolase 1ecto-ATPDase 1ecto-ATPase 1ecto-apyraselymphoid cell activation antigen
	Modification date	20141222
dbXrefs	MIM : 601752
	HGNC : HGNC
	Ensembl : ENSG00000138185
	HPRD : 09047
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ENTPD1
	BioGPS: 953
	Gene Expression Atlas: ENSG00000138185
	The Human Protein Atlas: ENSG00000138185
Pathway	NCI Pathway Interaction Database: ENTPD1
	KEGG: ENTPD1
	REACTOME: ENTPD1
	ConsensusPathDB
	Pathway Commons: ENTPD1
Metabolism	MetaCyc: ENTPD1
	HUMANCyc: ENTPD1
Regulation	Ensembl's Regulation: ENSG00000138185
	miRBase: chr10 :97,515,672-97,637,023
	TargetScan: NM_001098175
	cisRED: ENSG00000138185
Context	iHOP: ENTPD1
	cancer metabolism search in PubMed: ENTPD1
	UCL Cancer Institute: ENTPD1
Assigned class in ccmGDB	C

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Phenotypic Information for ENTPD1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ENTPD1
	Familial Cancer Database: ENTPD1

* 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_PURINE_METABOLISM KEGG_PYRIMIDINE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: ENTPD1
	MedGen: ENTPD1 (Human Medical Genetics with Condition)
	ClinVar: ENTPD1
Phenotype	MGI: ENTPD1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ENTPD1

Mutations for ENTPD1

* 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 ENTPD1 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
DA313964	RTN4	1	86	2	55199667	55199752	ENTPD1	87	550	10	97515920	97602224
DR006627	PRKACA	23	456	19	14217572	14228556	ENTPD1	452	694	10	97627439	97627682
AW581220	ENTPD1	1	75	10	97626002	97626077	ENTPD1	70	277	10	97626056	97626263
BF374130	ENTPD1	1	198	10	97552892	97553089	IKZF1	193	320	7	50470625	50470752
BE796741	ENTPD1	102	125	10	97485323	97485346	RPL13	120	751	16	89627137	89628145
AV721912	ENTPD1	28	613	10	97593265	97633514	ENTPD1	610	719	10	97594369	97594478
W80598	ENTPD1	114	133	10	97602912	97602931	DGKH	134	418	13	42811785	42812066

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

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

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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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=34)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

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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
chr10:97599530-97599530	p.G76D	2
chr10:97605259-97605259	p.R240H	2
chr10:97599541-97599541	p.Q80*	2
chr10:97599558-97599558	p.R85R	2
chr10:97607227-97607227	p.D280N	2
chr10:97602241-97602241	p.R135W	2
chr10:97607250-97607250	p.Y287Y	1
chr10:97599523-97599523	p.D74N	1
chr10:97620254-97620254	p.K368T	1
chr10:97604242-97604242	p.S141R	1

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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		8	2		3		1		1	5	2	1			11	7		5
# mutation		1		6	2		3		1		1	6	2	1			12	7		5
nonsynonymous SNV		1		4			2				1	6	2				10	5		3
synonymous SNV				2	2		1		1					1			2	2		2

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
chr10:97599530	p.D142N,ENTPD1	2
chr10:97605149	p.T65T,ENTPD1	2
chr10:97605259	p.G83D,ENTPD1	2
chr10:97607227	p.R102H,ENTPD1	2
chr10:97624518	p.G119E,ENTPD1	1
chr10:97599483	p.Y316H,ENTPD1	1
chr10:97604314	p.Q87E,ENTPD1	1
chr10:97607250	p.L358S,ENTPD1	1
chr10:97624583	p.Q87Q,ENTPD1	1
chr10:97607265	p.H146Y,ENTPD1	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 ENTPD1 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 ENTPD1

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


DCN,ECM2,ELK3,ENTPD1,F2R,FAM26E,FMNL3, GAS7,HEG1,KCTD12,KIAA1462,OLFML1,PLXNC1,RECK, PEAK1,SLIT2,TCF4,VCAN,WIPF1,ZEB1,ZEB2	ABCC4,CDH11,CHST15,CNTN4,CYP1B1,DNAJC10,ENTPD1, F2R,F2RL2,LRRC16A,MICAL2,MXRA5,MYO1E,PLXDC1, PLXNC1,SEC24D,SERPINE2,STARD4,TLR7,UGGT1,WWC3

VSTM4,C1S,CNRIP1,DZIP1,ENTPD1,FBXL7,FSTL1, GAS7,GNB4,GUCY1B3,LPHN2,MAF,OLFML1,PABPC5, PKD2,PTPRM,QKI,SYT11,TCF4,ZEB2,ZNF521	ACTA2,ACTG2,ACTN1,ANXA6,CASQ2,CNN1,CSRP1, ENTPD1,FHL3,RBFOX3,ILDR2,ILK,ITGB3,LGALS1, LOC100192378,NLGN1,PDLIM7,TAGLN,TMEM200B,TUBA1A,ZFHX4

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 ENTPD1

There's no related Drug.

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Cross referenced IDs for ENTPD1

* 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