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 ENTPD4

Basic gene info.	Gene symbol	ENTPD4
	Gene name	ectonucleoside triphosphate diphosphohydrolase 4
	Synonyms	LALP70\|LAP70\|LYSAL1\|NTPDase-4\|UDPase
	Cytomap	UCSC genome browser: 8p21.3
	Genomic location	chr8 :23286664-23315244
	Type of gene	protein-coding
	RefGenes	NM_001128930.2, NM_004901.4,
	Ensembl id	ENSG00000197217
	Description	golgi luminal UDPaseguanosine-diphosphatase like proteinlysosomal apyrase-like 1lysosomal apyrase-like protein of 70 kDauridine-diphosphatase
	Modification date	20141207
dbXrefs	MIM : 607577
	HGNC : HGNC
	Ensembl : ENSG00000197217
	HPRD : 09618
	Vega : OTTHUMG00000097852
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ENTPD4
	BioGPS: 9583
	Gene Expression Atlas: ENSG00000197217
	The Human Protein Atlas: ENSG00000197217
Pathway	NCI Pathway Interaction Database: ENTPD4
	KEGG: ENTPD4
	REACTOME: ENTPD4
	ConsensusPathDB
	Pathway Commons: ENTPD4
Metabolism	MetaCyc: ENTPD4
	HUMANCyc: ENTPD4
Regulation	Ensembl's Regulation: ENSG00000197217
	miRBase: chr8 :23,286,664-23,315,244
	TargetScan: NM_001128930
	cisRED: ENSG00000197217
Context	iHOP: ENTPD4
	cancer metabolism search in PubMed: ENTPD4
	UCL Cancer Institute: ENTPD4
Assigned class in ccmGDB	C

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Phenotypic Information for ENTPD4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ENTPD4
	Familial Cancer Database: ENTPD4

* 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: ENTPD4
	MedGen: ENTPD4 (Human Medical Genetics with Condition)
	ClinVar: ENTPD4
Phenotype	MGI: ENTPD4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ENTPD4

Mutations for ENTPD4

* 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 ENTPD4 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
AA465661	C17orf62	32	91	17	80400519	80400578	ENTPD4	82	370	8	23289140	23289429
BI001449	ENTPD4	7	222	8	23293720	23293935	ENTPD4	217	280	8	23293440	23293503
BF872346	ENTPD4	1	248	8	23297311	23299236	ENTPD4	239	292	8	23299526	23299579
BF084356	C14orf37	14	307	14	58686232	58686526	ENTPD4	299	383	8	23267941	23268025
BE932194	CNOT1	7	84	16	58589686	58589764	ENTPD4	80	276	8	23299520	23302001

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=44)	Stat. for Synonymous SNVs (# total SNVs=14)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr8:23305332-23305332	p.I91I	3
chr8:23306283-23306283	p.R60*	2
chr8:23292985-23292985	p.Y460Y	2
chr8:23290534-23290534	p.R586W	2
chr8:23301973-23301973	p.E187K	2
chr8:23294586-23294586	p.S412F	2
chr8:23305377-23305377	p.D76D	2
chr8:23305378-23305378	p.D76G	2
chr8:23290492-23290492	p.A600T	2
chr8:23291937-23291937	p.S505S	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		14			3		2			3	1	1		1	6	9		4
# mutation	1	3		13			3		2			4	1	1		1	7	10		5
nonsynonymous SNV		3		11			3		1			2					3	7		2
synonymous SNV	1			2					1			2	1	1		1	4	3		3

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
chr8:23305332	p.T430T,ENTPD4	2
chr8:23305378	p.A592T,ENTPD4	2
chr8:23291937	p.I91I,ENTPD4	2
chr8:23290492	p.D76G,ENTPD4	2
chr8:23294507	p.S497S,ENTPD4	2
chr8:23294509	p.A42V,ENTPD4	1
chr8:23299142	p.E187K,ENTPD4	1
chr8:23290619	p.T430A,ENTPD4	1
chr8:23294525	p.P186P,ENTPD4	1
chr8:23299143	p.A590A,ENTPD4	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 ENTPD4 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 ENTPD4

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


ASH1L,CNOT7,DOCK5,ENTPD4,HMBOX1,INTS9,KIF13B, MCPH1,MTMR9,PCM1,PPP2R2A,SH2D4A,TBC1D8B,TNFRSF10A, TNFRSF10B,TNKS,TOR1AIP2,VPS37A,WRN,XPO7,ZNF395	ARID1A,FAM208B,CCAR1,DCAF7,DHX15,DOCK5,ENTPD4, ENTPD7,EPT1,FGD6,GSTCD,AREL1,RCAN3,RPGRIP1L, SEC23IP,SLC9A7,NDC1,TP53BP1,TRRAP,ZBED4,ZNF8

ASAH1,ATP6V1B2,CHMP7,DOCK5,ENTPD4,EXTL3,FAM160B2, HMBOX1,CCAR2,KIF13B,MFHAS1,MTMR9,MTUS1,PCM1, POLR3D,PSD3,TNFRSF10A,TNKS,TRIM35,VPS37A,XPO7	APAF1,ATP11B,AVL9,BAZ2A,C10orf12,PRR14L,CSNK1G1, DEPDC5,DIP2B,ENTPD4,FAM160A1,GOLGA3,IQGAP1,MAP3K9, MYO18A,NCOR1,PIK3C2B,PLEKHA6,PPFIA1,RRBP1,ZCCHC6

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 ENTPD4

There's no related Drug.

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Cross referenced IDs for ENTPD4

* 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