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 ENTPD4
Basic gene info.Gene symbolENTPD4
Gene nameectonucleoside triphosphate diphosphohydrolase 4
SynonymsLALP70|LAP70|LYSAL1|NTPDase-4|UDPase
CytomapUCSC genome browser: 8p21.3
Genomic locationchr8 :23286664-23315244
Type of geneprotein-coding
RefGenesNM_001128930.2,
NM_004901.4,
Ensembl idENSG00000197217
Descriptiongolgi luminal UDPaseguanosine-diphosphatase like proteinlysosomal apyrase-like 1lysosomal apyrase-like protein of 70 kDauridine-diphosphatase
Modification date20141207
dbXrefs MIM : 607577
HGNC : HGNC
Ensembl : ENSG00000197217
HPRD : 09618
Vega : OTTHUMG00000097852
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ENTPD4
BioGPS: 9583
Gene Expression Atlas: ENSG00000197217
The Human Protein Atlas: ENSG00000197217
PathwayNCI Pathway Interaction Database: ENTPD4
KEGG: ENTPD4
REACTOME: ENTPD4
ConsensusPathDB
Pathway Commons: ENTPD4
MetabolismMetaCyc: ENTPD4
HUMANCyc: ENTPD4
RegulationEnsembl's Regulation: ENSG00000197217
miRBase: chr8 :23,286,664-23,315,244
TargetScan: NM_001128930
cisRED: ENSG00000197217
ContextiHOP: ENTPD4
cancer metabolism search in PubMed: ENTPD4
UCL Cancer Institute: ENTPD4
Assigned class in ccmGDBC

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Phenotypic Information for ENTPD4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_PURINE_METABOLISM
KEGG_PYRIMIDINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ENTPD4
MedGen: ENTPD4 (Human Medical Genetics with Condition)
ClinVar: ENTPD4
PhenotypeMGI: ENTPD4 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ENTPD4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA465661C17orf623291178040051980400578ENTPD48237082328914023289429
BI001449ENTPD4722282329372023293935ENTPD421728082329344023293503
BF872346ENTPD4124882329731123299236ENTPD423929282329952623299579
BF084356C14orf3714307145868623258686526ENTPD429938382326794123268025
BE932194CNOT1784165858968658589764ENTPD48027682329952023302001

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 # sample      1          
GAIN (# sample)                 
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=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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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
chr8:23305332-23305332p.I91I3
chr8:23306283-23306283p.R60*2
chr8:23292985-23292985p.Y460Y2
chr8:23290534-23290534p.R586W2
chr8:23301973-23301973p.E187K2
chr8:23294586-23294586p.S412F2
chr8:23305377-23305377p.D76D2
chr8:23305378-23305378p.D76G2
chr8:23290492-23290492p.A600T2
chr8:23291937-23291937p.S505S2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13 14  3 2  311 169 4
# mutation13 13  3 2  411 1710 5
nonsynonymous SNV 3 11  3 1  2    37 2
synonymous SNV1  2    1  211 143 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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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
chr8:23305332p.I91I,ENTPD42
chr8:23305378p.D76G,ENTPD42
chr8:23291937p.S497S,ENTPD42
chr8:23290492p.T430T,ENTPD42
chr8:23294507p.A592T,ENTPD42
chr8:23294509p.F334L,ENTPD41
chr8:23299142p.G549G,ENTPD41
chr8:23290619p.R332K,ENTPD41
chr8:23294525p.G90E,ENTPD41
chr8:23299143p.R548Q,ENTPD41

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 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

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

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
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 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



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