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 ENPP3

Basic gene info.	Gene symbol	ENPP3
	Gene name	ectonucleotide pyrophosphatase/phosphodiesterase 3
	Synonyms	B10\|CD203c\|NPP3\|PD-IBETA\|PDNP3
	Cytomap	UCSC genome browser: 6q22
	Genomic location	chr6 :131958441-132068550
	Type of gene	protein-coding
	RefGenes	NM_005021.3,
	Ensembl id	ENSG00000154269
	Description	dJ1005H11.3 (phosphodiesterase I/nucleotide pyrophosphatase 3)dJ914N13.3 (phosphodiesterase I/nucleotide pyrophosphatase 3)ectonucleotide pyrophosphatase/phosphodiesterase family member 3gp130RB13-6phosphodiesterase I/nucleotide pyrophosphatase 3phos
	Modification date	20141222
dbXrefs	MIM : 602182
	HGNC : HGNC
	Ensembl : ENSG00000154269
	HPRD : 03715
	Vega : OTTHUMG00000016292
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ENPP3
	BioGPS: 5169
	Gene Expression Atlas: ENSG00000154269
	The Human Protein Atlas: ENSG00000154269
Pathway	NCI Pathway Interaction Database: ENPP3
	KEGG: ENPP3
	REACTOME: ENPP3
	ConsensusPathDB
	Pathway Commons: ENPP3
Metabolism	MetaCyc: ENPP3
	HUMANCyc: ENPP3
Regulation	Ensembl's Regulation: ENSG00000154269
	miRBase: chr6 :131,958,441-132,068,550
	TargetScan: NM_005021
	cisRED: ENSG00000154269
Context	iHOP: ENPP3
	cancer metabolism search in PubMed: ENPP3
	UCL Cancer Institute: ENPP3
Assigned class in ccmGDB	C

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Phenotypic Information for ENPP3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ENPP3
	Familial Cancer Database: ENPP3

* 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_STARCH_AND_SUCROSE_METABOLISM KEGG_RIBOFLAVIN_METABOLISM KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: ENPP3
	MedGen: ENPP3 (Human Medical Genetics with Condition)
	ClinVar: ENPP3
Phenotype	MGI: ENPP3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ENPP3

Mutations for ENPP3

* 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	ENPP3	chr6	132014038	132014238	ENPP3	chr6	132013900	132014100
ovary	ENPP3	chr6	132036863	132037063		chr7	143442572	143442772

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 ENPP3 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
BF361277	YWHAQ	7	404	2	9725010	9725406	ENPP3	386	488	6	132062737	132062839
BE936958	YWHAQ	1	364	2	9725010	9725373	ENPP3	346	448	6	132062737	132062839

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=81)	Stat. for Synonymous SNVs (# total SNVs=22)

Stat. for Deletions (# total SNVs=4)	Stat. for Insertions (# total SNVs=0)
	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
chr6:131973708-131973708	p.R102C	4
chr6:131995408-131995408	p.W250*	3
chr6:132014640-132014640	p.R430*	3
chr6:132014722-132014722	p.D457G	3
chr6:132059248-132059248	p.P749T	2
chr6:132006591-132006591	p.R405fs*36	2
chr6:132054739-132054739	p.S655S	2
chr6:132054817-132054817	p.F681L	2
chr6:131995407-131995407	p.W250R	2
chr6:132068022-132068022	p.Q852*	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	3	3	1	9			7		3			14	7	2		2	15	5		14
# mutation	3	3	1	9			7		3			16	7	2		2	13	5		22
nonsynonymous SNV	1	2	1	6			5		1			14	4	1		2	11	4		18
synonymous SNV	2	1		3			2		2			2	3	1			2	1		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
chr6:131973708	p.R102C	3
chr6:132047338	p.W250R	2
chr6:131995407	p.L651L	2
chr6:132014759	p.F395F	1
chr6:131958539	p.G480E	1
chr6:131995398	p.D703Y	1
chr6:132047311	p.T9T	1
chr6:131971206	p.E109K	1
chr6:131999049	p.A248S	1
chr6:132006597	p.Y397C	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 ENPP3 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 ENPP3

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


ACSM1,C15orf43,LINC00589,ENPP3,GGT1,GJB1,ISX, MAP10,KRT40,KRTAP1-3,KRTAP1-5,KRTAP3-2,KRTAP3-3,NPY6R, OXER1,SCP2,SIPA1L2,SLC38A4,TMIGD1,UGT3A2,ZNRF3	ACSL3,ADAM2,ALOX15B,APOD,DHRS2,ENPP3,F9, GUSB,HAAO,HIST1H3D,HIST1H4H,IDI1,NANOG,NAT2, PLA2G4E,PPEF1,RNASE12,SERHL,SPINK8,SULT1C3,UGT2B11

APOLD1,BCL11A,TEX43,CD46,CEP68,CFTR,ENPP3, GPSM2,MYO10,NAALADL2,OXGR1,PLCB4,RGR,RNF43, SATB2,SH3BP4,SRGAP3,TDGF1,TEAD2,TMEM150C,TRAF5	SOWAHA,ANPEP,AQP11,CA13,CDHR2,CDHR5,CYP2B6, ENPP3,FLVCR1,HNF4G,ING2,LOC148709,MEP1A,MSRA, MYO1A,PCK2,PLCB3,PRAP1,SLC3A1,SLC46A3,AGMO

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 ENPP3

There's no related Drug.

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Cross referenced IDs for ENPP3

* 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