Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 ENPP1
Basic gene info.Gene symbolENPP1
Gene nameectonucleotide pyrophosphatase/phosphodiesterase 1
SynonymsARHR2|COLED|M6S1|NPP1|NPPS|PC-1|PCA1|PDNP1
CytomapUCSC genome browser: 6q22-q23
Genomic locationchr6 :132129155-132216295
Type of geneprotein-coding
RefGenesNM_006208.2,
Ensembl idENSG00000197594
DescriptionE-NPP 1Ly-41 antigenalkaline phosphodiesterase 1ectonucleotide pyrophosphatase/phosphodiesterase family member 1membrane component chromosome 6 surface marker 1membrane component, chromosome 6, surface marker 1phosphodiesterase I/nucleotide pyrophos
Modification date20141222
dbXrefs MIM : 173335
HGNC : HGNC
Ensembl : ENSG00000197594
HPRD : 01415
Vega : OTTHUMG00000015572
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ENPP1
BioGPS: 5167
Gene Expression Atlas: ENSG00000197594
The Human Protein Atlas: ENSG00000197594
PathwayNCI Pathway Interaction Database: ENPP1
KEGG: ENPP1
REACTOME: ENPP1
ConsensusPathDB
Pathway Commons: ENPP1
MetabolismMetaCyc: ENPP1
HUMANCyc: ENPP1
RegulationEnsembl's Regulation: ENSG00000197594
miRBase: chr6 :132,129,155-132,216,295
TargetScan: NM_006208
cisRED: ENSG00000197594
ContextiHOP: ENPP1
cancer metabolism search in PubMed: ENPP1
UCL Cancer Institute: ENPP1
Assigned class in ccmGDBC

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Phenotypic Information for ENPP1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ENPP1
Familial Cancer Database: ENPP1
* 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/

check002.gifMetabolic Pathway Description
KEGG_PURINE_METABOLISM
KEGG_STARCH_AND_SUCROSE_METABOLISM
KEGG_RIBOFLAVIN_METABOLISM
KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM
REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ENPP1
MedGen: ENPP1 (Human Medical Genetics with Condition)
ClinVar: ENPP1
PhenotypeMGI: ENPP1 (International Mouse Phenotyping Consortium)
PhenomicDB: ENPP1

Mutations for ENPP1
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ENPP1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1     1          
GAIN (# sample)1                
LOSS (# sample)      1          
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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check002.gifSNV 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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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=88)
Stat. for Synonymous SNVs
(# total SNVs=19)
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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr6:132193231-132193231p.R424Q4
chr6:132211590-132211590p.E854G4
chr6:132201173-132201173p.N648S3
chr6:132211563-132211563p.G845E3
chr6:132190590-132190590p.R404*2
chr6:132206138-132206138p.V741V2
chr6:132171205-132171205p.G78E2
chr6:132204911-132204911p.Q718*2
chr6:132194055-132194055p.?2
chr6:132203595-132203595p.Y685Y2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample33 171 5 31 1274 2165111
# mutation33 171 5 31 1383 2165113
nonsynonymous SNV23 111 4 11 1062  104111
synonymous SNV1  6  1 2  321 261 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr6:132211590p.E906G4
chr6:132171147p.R111C3
chr6:132203595p.V793V2
chr6:132206138p.Y737Y2
chr6:132207750p.F831F2
chr6:132203589p.L232F1
chr6:132211593p.K445T1
chr6:132181527p.S694S1
chr6:132190558p.K783T1
chr6:132206107p.G871V1

check002.gifOther 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

check002.gifCopy Number for ENPP1 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 ENPP1

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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

AIM1,ATG5,SMIM14,C6orf203,LINC00589,ENPP1,FOXA1,
GOLGA1,KCTD3,KRT40,KRTAP1-3,KRTAP3-2,KRTAP3-3,MAN1A1,
MED23,NEDD1,PDSS2,SIPA1L2,STX7,XBP1,ZNRF3
AHCYL1,AIG1,ATP9A,BNIP3L,CDKN2B,CREBL2,ENPP1,
HNMT,HSD17B4,JAK1,MAOA,NEK7,PARVA,PTP4A2,
RGS22,RHOBTB3,SESTD1,SH3D19,SORT1,STX12,TRAK2

ACHE,B3GALT4,VWA7,CDHR5,CEACAM5,CHAD,CLDN23,
CTSA,EDN3,ENPP1,TMEM236,GRN,LOC283267,NAAA,
PRKCD,SEPP1,SNX9,STBD1,TMEM133,TP53INP2,YPEL3
ACOX1,APPL2,ATP1B1,BAHD1,STPG1,CDKN2B,CGN,
RHOV___CHP1,CLCN2,ENPP1,ABHD17C,GBA,IST1,MAST2,
MGLL,MYO15B,PEX26,RNF103,SFXN1,TMEM127,WASL
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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 ENPP1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00811ectonucleotide pyrophosphatase/phosphodiesterase 1approvedRibavirin
DB01143ectonucleotide pyrophosphatase/phosphodiesterase 1approved; investigationalAmifostine
DB00131ectonucleotide pyrophosphatase/phosphodiesterase 1approved; nutraceuticalAdenosine monophosphate
DB00171ectonucleotide pyrophosphatase/phosphodiesterase 1approved; nutraceuticalAdenosine triphosphate


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Cross referenced IDs for ENPP1
* 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



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