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 ITPA
Basic gene info.Gene symbolITPA
Gene nameinosine triphosphatase (nucleoside triphosphate pyrophosphatase)
SynonymsC20orf37|HLC14-06-P|dJ794I6.3
CytomapUCSC genome browser: 20p
Genomic locationchr20 :3190055-3204506
Type of geneprotein-coding
RefGenesNM_001267623.1,
NM_033453.3,NM_181493.2,NR_052000.1,NR_052001.1,
NR_052002.1,
Ensembl idENSG00000125877
DescriptionITPaseNTPaseinosine triphosphatase-Ainosine triphosphate pyrophosphataseinosine triphosphate pyrophosphohydrolasenon-canonical purine NTP pyrophosphatasenon-standard purine NTP pyrophosphatasenucleoside-triphosphate diphosphataseputative oncogene
Modification date20141207
dbXrefs MIM : 147520
HGNC : HGNC
Ensembl : ENSG00000125877
HPRD : 08856
Vega : OTTHUMG00000031738
ProteinUniProt: Q9BY32
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ITPA
BioGPS: 3704
Gene Expression Atlas: ENSG00000125877
The Human Protein Atlas: ENSG00000125877
PathwayNCI Pathway Interaction Database: ITPA
KEGG: ITPA
REACTOME: ITPA
ConsensusPathDB
Pathway Commons: ITPA
MetabolismMetaCyc: ITPA
HUMANCyc: ITPA
RegulationEnsembl's Regulation: ENSG00000125877
miRBase: chr20 :3,190,055-3,204,506
TargetScan: NM_001267623
cisRED: ENSG00000125877
ContextiHOP: ITPA
cancer metabolism search in PubMed: ITPA
UCL Cancer Institute: ITPA
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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

check002.gifOthers
OMIM 147520; gene.
147520; gene.
613850; phenotype.
613850; phenotype.
Orphanet 284113; Susceptibility to adverse reaction due to mercaptopurine.
284113; Susceptibility to adverse reaction due to mercaptopurine.
319684; Inosine triphosphatase deficiency.
319684; Inosine triphosphatase deficiency.
DiseaseKEGG Disease: ITPA
MedGen: ITPA (Human Medical Genetics with Condition)
ClinVar: ITPA
PhenotypeMGI: ITPA (International Mouse Phenotyping Consortium)
PhenomicDB: ITPA

Mutations for ITPA
* 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 ITPA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM545059ITPA1842182032042253204259ITPA2186562031901753199279

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)          1      
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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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=16)
Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr20:3202495-3202495p.I140I3
chr20:3194652-3194652p.E71K2
chr20:3194676-3194676p.A79T2
chr20:3193818-3193818p.V24I2
chr20:3193840-3193840p.F31C1
chr20:3193842-3193842p.P32T1
chr20:3202497-3202497p.V141G1
chr20:3193865-3193865p.K39N1
chr20:3202514-3202514p.Q147*1
chr20:3193968-3193968p.P43L1

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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
# sample   5  2    1 1  32 1
# mutation   5  2    1 1  22 1
nonsynonymous SNV   4  2    1 1     1
synonymous SNV   1            22  
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
chr20:3194676p.A38T,ITPA2
chr20:3202495p.I99I,ITPA2
chr20:3193981p.Y147D,ITPA1
chr20:3194643p.V24I,ITPA1
chr20:3194649p.K39N,ITPA1
chr20:3199166p.I40M,ITPA1
chr20:3199170p.G47G,ITPA1
chr20:3204033p.V27M,ITPA1
chr20:3193818p.V29F,ITPA1
chr20:3204042p.L59R,ITPA1

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 ITPA 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 ITPA

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

BCL7C,C19orf70,C20orf27,CCDC12,CCDC124,CDC34,CENPB,
GADD45GIP1,GUK1,IDH3B,ITPA,LSM7,MRPL23,MRPS26,
LINC00116,NDUFA11,NDUFA13,NDUFB7,RPS19BP1,SNRPB,ZNHIT1
APRT,BRMS1,CHID1,COMMD5,DTYMK,EIF6,EXOSC4,
ITPA,LSM7,MAZ,NHP2,PES1,PPP4C,PRPF31,
PSMG3,PUS1,RALY,RUVBL2,STRA13,SURF2,TMEM208

C20orf27,AP5S1,TMEM230,CRLS1,DDRGK1,FAM110A,FKBP1A,
IDH3B,ITPA,MKKS,MRPS26,NOP56,NSFL1C,PANK2,
PCNA,PSMF1,SNRPB,TRMT6,UBOX5,VPS16,ZCCHC3
ABT1,AHCY,APTX,BID,C16orf91,CDC123,COA4,
CYC1,DCTPP1,ITPA,LSM7,MRPS12,MTFP1,POP5,
PSMG3,SF3B5,SNRPB,TARBP2,TIMM13,PAM16,TMX2
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 ITPA
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA29973; -.
Organism-specific databasesPharmGKB PA29973; -.
Organism-specific databasesCTD 3704; -.
Organism-specific databasesCTD 3704; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01033inosine triphosphatase (nucleoside triphosphate pyrophosphatase)approvedMercaptopurine
DB00563inosine triphosphatase (nucleoside triphosphate pyrophosphatase)approvedMethotrexate
DB00993inosine triphosphatase (nucleoside triphosphate pyrophosphatase)approvedAzathioprine
DB00158inosine triphosphatase (nucleoside triphosphate pyrophosphatase)approved; nutraceuticalFolic Acid


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Cross referenced IDs for ITPA
* 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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