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 PNPT1
Basic gene info.Gene symbolPNPT1
Gene namepolyribonucleotide nucleotidyltransferase 1
SynonymsCOXPD13|DFNB70|OLD35|PNPASE|old-35
CytomapUCSC genome browser: 2p15
Genomic locationchr2 :55861197-55921011
Type of geneprotein-coding
RefGenesNM_033109.4,
Ensembl idENSG00000138035
Description3'-5' RNA exonuclease OLD35PNPase 1PNPase old-35polynucleotide phosphorylase 1polynucleotide phosphorylase-like proteinpolyribonucleotide nucleotidyltransferase 1, mitochondrial
Modification date20141207
dbXrefs MIM : 610316
HGNC : HGNC
Ensembl : ENSG00000138035
HPRD : 18493
Vega : OTTHUMG00000129335
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PNPT1
BioGPS: 87178
Gene Expression Atlas: ENSG00000138035
The Human Protein Atlas: ENSG00000138035
PathwayNCI Pathway Interaction Database: PNPT1
KEGG: PNPT1
REACTOME: PNPT1
ConsensusPathDB
Pathway Commons: PNPT1
MetabolismMetaCyc: PNPT1
HUMANCyc: PNPT1
RegulationEnsembl's Regulation: ENSG00000138035
miRBase: chr2 :55,861,197-55,921,011
TargetScan: NM_033109
cisRED: ENSG00000138035
ContextiHOP: PNPT1
cancer metabolism search in PubMed: PNPT1
UCL Cancer Institute: PNPT1
Assigned class in ccmGDBC

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Phenotypic Information for PNPT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PNPT1
Familial Cancer Database: PNPT1
* 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: PNPT1
MedGen: PNPT1 (Human Medical Genetics with Condition)
ClinVar: PNPT1
PhenotypeMGI: PNPT1 (International Mouse Phenotyping Consortium)
PhenomicDB: PNPT1

Mutations for PNPT1
* 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 PNPT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI025641PNPT1331025589848055906852PNPT130439025589414455894230
BF895069PNPT1134125589969755900040ASAP13344478131065683131065796
BQ378709PNPT1939225588205455894211PNPT139164625587357955883319
BQ335094PNPT1532325589848055906864PNPT131738725589414455894214

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=60)
Stat. for Synonymous SNVs
(# total SNVs=12)
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
chr2:55874526-55874526p.E520Q3
chr2:55883470-55883470p.T441A2
chr2:55900055-55900055p.S280L2
chr2:55895069-55895069p.Y334C2
chr2:55863468-55863468p.L752L2
chr2:55863478-55863478p.R749Q2
chr2:55863483-55863483p.L747L2
chr2:55872496-55872496p.G604*1
chr2:55894205-55894205p.S366L1
chr2:55912132-55912132p.L117V1

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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
# sample23 91 2 12 43   38 5
# mutation23 121 2 12 43   39 6
nonsynonymous SNV13 121 2  2 31   15 6
synonymous SNV1       1  12   24  
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
chr2:55894127p.R749Q2
chr2:55863478p.Q392L2
chr2:55908004p.Q74R1
chr2:55870530p.N603H1
chr2:55883311p.Y334S1
chr2:55898455p.P333P1
chr2:55912132p.V49V1
chr2:55870544p.L586V1
chr2:55883321p.A331A1
chr2:55899142p.A37S1

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 PNPT1 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 PNPT1

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 PNPT1


There's no related Drug.
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Cross referenced IDs for PNPT1
* 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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