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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for NUDT5 |
Basic gene info. | Gene symbol | NUDT5 |
Gene name | nudix (nucleoside diphosphate linked moiety X)-type motif 5 | |
Synonyms | YSA1|YSA1H|YSAH1|hYSAH1 | |
Cytomap | UCSC genome browser: 10p14 | |
Genomic location | chr10 :12209572-12238143 | |
Type of gene | protein-coding | |
RefGenes | NM_014142.2, | |
Ensembl id | ENSG00000165609 | |
Description | 8-oxo-dGDP phosphataseADP-sugar pyrophosphatase | |
Modification date | 20141207 | |
dbXrefs | MIM : 609230 | |
HGNC : HGNC | ||
Ensembl : ENSG00000165609 | ||
HPRD : 14851 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_NUDT5 | |
BioGPS: 11164 | ||
Gene Expression Atlas: ENSG00000165609 | ||
The Human Protein Atlas: ENSG00000165609 | ||
Pathway | NCI Pathway Interaction Database: NUDT5 | |
KEGG: NUDT5 | ||
REACTOME: NUDT5 | ||
ConsensusPathDB | ||
Pathway Commons: NUDT5 | ||
Metabolism | MetaCyc: NUDT5 | |
HUMANCyc: NUDT5 | ||
Regulation | Ensembl's Regulation: ENSG00000165609 | |
miRBase: chr10 :12,209,572-12,238,143 | ||
TargetScan: NM_014142 | ||
cisRED: ENSG00000165609 | ||
Context | iHOP: NUDT5 | |
cancer metabolism search in PubMed: NUDT5 | ||
UCL Cancer Institute: NUDT5 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for NUDT5(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: NUDT5 |
Familial Cancer Database: NUDT5 |
* This gene is included in those cancer gene databases. |
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/ |
Metabolic Pathway Description | |
KEGG_PURINE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: NUDT5 |
MedGen: NUDT5 (Human Medical Genetics with Condition) | |
ClinVar: NUDT5 | |
Phenotype | MGI: NUDT5 (International Mouse Phenotyping Consortium) |
PhenomicDB: NUDT5 |
Mutations for NUDT5 |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NUDT5 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 |
DC322982 | NUDT5 | 1 | 214 | 10 | 12228228 | 12237878 | ZMYND11 | 213 | 554 | 10 | 225932 | 282822 | |
DA370758 | NUDT5 | 1 | 172 | 10 | 12214050 | 12214221 | WDR90 | 169 | 562 | 16 | 714964 | 715407 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=11) | (# total SNVs=3) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr10:12209739-12209739 | p.N208D | 2 |
chr10:12209752-12209752 | p.A203A | 2 |
chr10:12215790-12215790 | p.T104T | 1 |
chr10:12215795-12215795 | p.E103K | 1 |
chr10:12219831-12219831 | p.R84* | 1 |
chr10:12219893-12219893 | p.A63V | 1 |
chr10:12209745-12209745 | p.H206N | 1 |
chr10:12221127-12221127 | p.W46R | 1 |
chr10:12226925-12226925 | p.E32Q | 1 |
chr10:12212721-12212721 | p.L182R | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   | 1 |   | 1 |   |   | 1 |   |   |   |   | 3 |   | 1 |   |   | 1 | 1 | 1 | 2 |
# mutation |   | 1 |   | 1 |   |   | 1 |   |   |   |   | 3 |   | 1 |   |   | 1 | 1 | 1 | 2 |
nonsynonymous SNV |   | 1 |   |   |   |   | 1 |   |   |   |   | 2 |   | 1 |   |   | 1 | 1 |   | 2 |
synonymous SNV |   |   |   | 1 |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr10:12219884 | p.A124A | 1 |
chr10:12221106 | p.T104T | 1 |
chr10:12221127 | p.E103K | 1 |
chr10:12209745 | p.P66L | 1 |
chr10:12228244 | p.T53A | 1 |
chr10:12212721 | p.W46R | 1 |
chr10:12212732 | p.Y16C | 1 |
chr10:12212901 | p.H206N | 1 |
chr10:12214779 | p.L182R | 1 |
chr10:12215730 | p.L178L | 1 |
Other DBs for Point Mutations |
Copy Number for NUDT5 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 NUDT5 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
ATP5C1,AURKB,CDC123,CDCA3,DCLRE1C,DHTKD1,FBXO18, GDI2,GTPBP4,HSPA14,KIN,MCM10,NUDT5,PDSS1, PRPF18,RBM17,RPP38,RSU1,SEPHS1,SNRPG,SUV39H2 | ACOT4,ANXA2,ANXA2P2,BCAP31,COPRS,SMIM7,CD63, FAIM,FAM32A,FUCA2,LSM1,MED8,MYL6,NUDT5, PDZD11,PEA15,PGAM1,POP4,RNF130,SNX11,SURF4 |
ATP5C1,CDC123,CDK1,CKS1B,DTYMK,GDI2,GTPBP4, HNRNPF,HSPA14,MCM10,MTPAP,NDUFAB1,NUDT5,PDSS1, RBM17,RFC4,RPP38,SEPHS1,SPC25,SUV39H2,UBE2T | CDK1,CHEK2,DDOST,MTFR2,GINS2,H2AFZ,ILF2, KIAA0101,MAD2L1,NUDT5,NUF2,NUP85,PCNA,RAD51AP1, RANBP1,RPL26L1,RPN1,SEC61B,SNRPB,SNRPD3,UBE2T |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for NUDT5 |
There's no related Drug. |
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Cross referenced IDs for NUDT5 |
* 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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