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 PNP
Basic gene info.Gene symbolPNP
Gene namepurine nucleoside phosphorylase
SynonymsNP|PRO1837|PUNP
CytomapUCSC genome browser: 14q13.1
Genomic locationchr14 :20937537-20946165
Type of geneprotein-coding
RefGenesNM_000270.3,
Ensembl idENSG00000198805
DescriptionHEL-S-156anepididymis secretory sperm binding protein Li 156aninosine phosphorylaseinosine-guanosine phosphorylasepurine-nucleoside:orthophosphate ribosyltransferase
Modification date20141221
dbXrefs MIM : 164050
HGNC : HGNC
HPRD : 01247
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PNP
BioGPS: 4860
Gene Expression Atlas: ENSG00000198805
The Human Protein Atlas: ENSG00000198805
PathwayNCI Pathway Interaction Database: PNP
KEGG: PNP
REACTOME: PNP
ConsensusPathDB
Pathway Commons: PNP
MetabolismMetaCyc: PNP
HUMANCyc: PNP
RegulationEnsembl's Regulation: ENSG00000198805
miRBase: chr14 :20,937,537-20,946,165
TargetScan: NM_000270
cisRED: ENSG00000198805
ContextiHOP: PNP
cancer metabolism search in PubMed: PNP
UCL Cancer Institute: PNP
Assigned class in ccmGDBC

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Phenotypic Information for PNP(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PNP
Familial Cancer Database: PNP
* 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_NICOTINATE_AND_NICOTINAMIDE_METABOLISM
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PURINE_METABOLISM

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

Mutations for PNP
* 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 PNP related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AF116670SUV420H11275116794456467944838PNP2661085142094329920945248
BQ315891PNP2151142094489520945047RAB7A1513243128516859128525334
AI064779APOA2214941161192082161193418PNP492553142094493020944991
AI133239SUV420H11275116794456467944838PNP266669142094329920944832

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=14)
Stat. for Synonymous SNVs
(# total SNVs=2)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr14:20940606-20940606p.G51S2
chr14:20943103-20943103p.E153K2
chr14:20943360-20943360p.E201K2
chr14:20940544-20940545p.I30fs*101
chr14:20943058-20943058p.L138L1
chr14:20943378-20943378p.R207C1
chr14:20943064-20943064p.G140C1
chr14:20943404-20943404p.D215D1
chr14:20940624-20940624p.P57S1
chr14:20944590-20944590p.R234*1

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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   4    11 2 1  41 1
# mutation   3    11 2 1  41 1
nonsynonymous SNV   3    11 1 1  2   
synonymous SNV           1    21 1
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
chr14:20943370p.A204V2
chr14:20940624p.P57S1
chr14:20940628p.R58Q1
chr14:20943404p.R58R1
chr14:20940629p.A77A1
chr14:20944608p.K95M1
chr14:20942680p.L138L1
chr14:20942733p.G140C1
chr14:20943058p.R158H1
chr14:20943064p.Q172Q1

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 PNP 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 PNP

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

BUB1,CEBPZ,CENPA,DBF4,EIF2AK2,FAM136A,GTPBP4,
IFIH1,MASTL,MSH2,MTIF2,NOP58,PNO1,PNPT1,
PTCD3,PUS7,SUV39H2,TTK,WDR12,WDR43,XPO1
ANKRD28,C5orf22,TRAPPC13,CUL3,DHX29,DHX36,DNM1L,
ESF1,FASTKD2,HSPA14,IBTK,KRR1,MFN1,NAA15,
OTUD6B,PATL1,PNPT1,RRP15,SLC30A9,UBE3A,UTP15

NDUFAF7,CCDC138,CEBPZ,CPSF3,DDX18,HSPD1,HSPE1,
LRPPRC,MEMO1,MRPL19,MRPL30,MTIF2,PNO1,PNPT1,
PTCD3,SSB,USP39,WDR12,WDR43,WDR75,ZC3H15
ABCE1,CCDC86,DDX21,DKC1,EXOSC9,FASTKD2,GNL2,
GTPBP4,MAK16,NIFK,NOP16,NOP58,ODC1,PIGW,
PNPT1,RCL1,SRSF2,SRSF7,TRMT6,WDR43,WDR77
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 PNP
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
DB00242purine nucleoside phosphorylaseapproved; investigationalCladribine
DB00900purine nucleoside phosphorylaseapprovedDidanosine
DB01667purine nucleoside phosphorylaseexperimental8-Azaguanine
DB02222purine nucleoside phosphorylaseexperimental2,6-Diamino-(S)-9-[2-(Phosphonomethoxy)Propyl]Purine
DB02230purine nucleoside phosphorylaseexperimentalImmucillin-G
DB02377purine nucleoside phosphorylaseexperimentalGuanine
DB02391purine nucleoside phosphorylaseexperimental2-Amino-7-[2-(2-Hydroxy-1-Hydroxymethyl-Ethylamino)-Ethyl]-1,7-Dihydro-Purin-6-One
DB02568purine nucleoside phosphorylaseexperimentalPeldesine
DB02796purine nucleoside phosphorylaseexperimental9-Deazainosine
DB02857purine nucleoside phosphorylaseexperimentalGuanosine
DB03101purine nucleoside phosphorylaseexperimentalRibose-1-Phosphate
DB03551purine nucleoside phosphorylaseexperimental4'-Deaza-1'-Aza-2'-Deoxy-1'-(9-Methylene)-Immucillin-H, (3r,4r)-N-[9-Deazahypoxanthin-9-Yl)Methyl]-4-Hydroxymethyl-Pyrrolidin-3-Ol
DB03609purine nucleoside phosphorylaseexperimental3-Deoxyguanosine
DB03881purine nucleoside phosphorylaseexperimentalMT-Immucillin-H
DB04076purine nucleoside phosphorylaseexperimentalHypoxanthine
DB04260purine nucleoside phosphorylaseexperimental9-(5,5-Difluoro-5-Phosphonopentyl)Guanine
DB04753purine nucleoside phosphorylaseexperimental9-DEAZAINOSINE-2',3'-O-ETHYLIDENEPHOSPHONATE
DB04754purine nucleoside phosphorylaseexperimentalGUANOSINE-2',3'-O-ETHYLIDENEPHOSPHONATE
DB04757purine nucleoside phosphorylaseexperimentalGUANOSINE-2',3'-O-METHYLIDENEPHOSPHONATE
DB03411purine nucleoside phosphorylaseexperimental2-Hydroxymethyl-Pyrrolidine-3,4-Diol
DB04095purine nucleoside phosphorylaseexperimental9-Deazahypoxanthine
DB02985purine nucleoside phosphorylaseexperimental8-Iodo-Guanine


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Cross referenced IDs for PNP
* 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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