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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PNPT1 |
Basic gene info. | Gene symbol | PNPT1 |
Gene name | polyribonucleotide nucleotidyltransferase 1 | |
Synonyms | COXPD13|DFNB70|OLD35|PNPASE|old-35 | |
Cytomap | UCSC genome browser: 2p15 | |
Genomic location | chr2 :55861197-55921011 | |
Type of gene | protein-coding | |
RefGenes | NM_033109.4, | |
Ensembl id | ENSG00000138035 | |
Description | 3'-5' RNA exonuclease OLD35PNPase 1PNPase old-35polynucleotide phosphorylase 1polynucleotide phosphorylase-like proteinpolyribonucleotide nucleotidyltransferase 1, mitochondrial | |
Modification date | 20141207 | |
dbXrefs | MIM : 610316 | |
HGNC : HGNC | ||
Ensembl : ENSG00000138035 | ||
HPRD : 18493 | ||
Vega : OTTHUMG00000129335 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PNPT1 | |
BioGPS: 87178 | ||
Gene Expression Atlas: ENSG00000138035 | ||
The Human Protein Atlas: ENSG00000138035 | ||
Pathway | NCI Pathway Interaction Database: PNPT1 | |
KEGG: PNPT1 | ||
REACTOME: PNPT1 | ||
ConsensusPathDB | ||
Pathway Commons: PNPT1 | ||
Metabolism | MetaCyc: PNPT1 | |
HUMANCyc: PNPT1 | ||
Regulation | Ensembl's Regulation: ENSG00000138035 | |
miRBase: chr2 :55,861,197-55,921,011 | ||
TargetScan: NM_033109 | ||
cisRED: ENSG00000138035 | ||
Context | iHOP: PNPT1 | |
cancer metabolism search in PubMed: PNPT1 | ||
UCL Cancer Institute: PNPT1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PNPT1(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PNPT1 |
Familial Cancer Database: PNPT1 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
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KEGG_PURINE_METABOLISM KEGG_PYRIMIDINE_METABOLISM |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: PNPT1 |
MedGen: PNPT1 (Human Medical Genetics with Condition) | |
ClinVar: PNPT1 | |
Phenotype | MGI: 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PNPT1 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BI025641 | PNPT1 | 3 | 310 | 2 | 55898480 | 55906852 | PNPT1 | 304 | 390 | 2 | 55894144 | 55894230 | |
BF895069 | PNPT1 | 1 | 341 | 2 | 55899697 | 55900040 | ASAP1 | 334 | 447 | 8 | 131065683 | 131065796 | |
BQ378709 | PNPT1 | 9 | 392 | 2 | 55882054 | 55894211 | PNPT1 | 391 | 646 | 2 | 55873579 | 55883319 | |
BQ335094 | PNPT1 | 5 | 323 | 2 | 55898480 | 55906864 | PNPT1 | 317 | 387 | 2 | 55894144 | 55894214 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
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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Stat. for Non-Synonymous SNVs (# total SNVs=60) | (# total SNVs=12) |
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(# total SNVs=0) | (# total SNVs=0) |
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* 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 position | Mutation(aa) | Unique sampleID count |
chr2:55874526-55874526 | p.E520Q | 3 |
chr2:55895069-55895069 | p.Y334C | 2 |
chr2:55863468-55863468 | p.L752L | 2 |
chr2:55863478-55863478 | p.R749Q | 2 |
chr2:55863483-55863483 | p.L747L | 2 |
chr2:55883470-55883470 | p.T441A | 2 |
chr2:55900055-55900055 | p.S280L | 2 |
chr2:55913533-55913533 | p.P90H | 1 |
chr2:55872517-55872517 | p.R597* | 1 |
chr2:55895051-55895051 | p.F340Y | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 2 | 3 |   | 9 | 1 |   | 2 |   | 1 | 2 |   | 4 | 3 |   |   |   | 3 | 8 |   | 5 |
# mutation | 2 | 3 |   | 12 | 1 |   | 2 |   | 1 | 2 |   | 4 | 3 |   |   |   | 3 | 9 |   | 6 |
nonsynonymous SNV | 1 | 3 |   | 12 | 1 |   | 2 |   |   | 2 |   | 3 | 1 |   |   |   | 1 | 5 |   | 6 |
synonymous SNV | 1 |   |   |   |   |   |   |   | 1 |   |   | 1 | 2 |   |   |   | 2 | 4 |   |   |
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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* 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 Position | Mutation(aa) | Unique sampleID count |
chr2:55894127 | p.R749Q | 2 |
chr2:55863478 | p.Q392L | 2 |
chr2:55900125 | p.R766T | 1 |
chr2:55872550 | p.I462M | 1 |
chr2:55920812 | p.A219G | 1 |
chr2:55894154 | p.S210Y | 1 |
chr2:55900192 | p.L448R | 1 |
chr2:55873404 | p.I195K | 1 |
chr2:55920850 | p.R715Q | 1 |
chr2:55894164 | p.G186G | 1 |
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* 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. |
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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 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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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 |
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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 |
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* 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 |
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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 |
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