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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for NT5M |
Basic gene info. | Gene symbol | NT5M |
Gene name | 5',3'-nucleotidase, mitochondrial | |
Synonyms | dNT-2|dNT2|mdN | |
Cytomap | UCSC genome browser: 17p11.2 | |
Genomic location | chr17 :17206679-17250977 | |
Type of gene | protein-coding | |
RefGenes | NM_020201.3, | |
Ensembl id | ENSG00000205309 | |
Description | 5' nucleotidase, mitochondrial5'(3')-deoxyribonucleotidase, mitochondrial5(3)-deoxyribonucleotidasedeoxy-5'-nucleotidase 2mitochondrial 5' nucleotidase | |
Modification date | 20141207 | |
dbXrefs | MIM : 605292 | |
HGNC : HGNC | ||
Ensembl : ENSG00000205309 | ||
HPRD : 12009 | ||
Vega : OTTHUMG00000059277 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_NT5M | |
BioGPS: 56953 | ||
Gene Expression Atlas: ENSG00000205309 | ||
The Human Protein Atlas: ENSG00000205309 | ||
Pathway | NCI Pathway Interaction Database: NT5M | |
KEGG: NT5M | ||
REACTOME: NT5M | ||
ConsensusPathDB | ||
Pathway Commons: NT5M | ||
Metabolism | MetaCyc: NT5M | |
HUMANCyc: NT5M | ||
Regulation | Ensembl's Regulation: ENSG00000205309 | |
miRBase: chr17 :17,206,679-17,250,977 | ||
TargetScan: NM_020201 | ||
cisRED: ENSG00000205309 | ||
Context | iHOP: NT5M | |
cancer metabolism search in PubMed: NT5M | ||
UCL Cancer Institute: NT5M | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for NT5M(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: NT5M |
Familial Cancer Database: NT5M |
* 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/ |
Metabolic Pathway Description | |
KEGG_PURINE_METABOLISM KEGG_PYRIMIDINE_METABOLISM KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PYRIMIDINE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: NT5M |
MedGen: NT5M (Human Medical Genetics with Condition) | |
ClinVar: NT5M | |
Phenotype | MGI: NT5M (International Mouse Phenotyping Consortium) |
PhenomicDB: NT5M |
Mutations for NT5M |
* 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 |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | NT5M | chr17 | 17212804 | 17212824 | ULK2 | chr17 | 19694755 | 19694775 |
ovary | NT5M | chr17 | 17224964 | 17224984 | ULK2 | chr17 | 19737489 | 19737509 |
pancreas | NT5M | chr17 | 17206877 | 17207077 | chr17 | 54040682 | 54040882 | |
prostate | NT5M | chr17 | 17243275 | 17243275 | PEMT | chr17 | 17428140 | 17428140 |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NT5M 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 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
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) | 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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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=5) |
(# total SNVs=1) | (# total SNVs=1) |
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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 |
chr17:17250250-17250250 | p.R226W | 2 |
chr17:17209886-17209886 | p.K99N | 2 |
chr17:17209911-17209911 | p.L108L | 1 |
chr17:17250123-17250123 | p.A183A | 1 |
chr17:17209922-17209922 | p.A111A | 1 |
chr17:17250185-17250185 | p.L204P | 1 |
chr17:17209934-17209934 | p.V115V | 1 |
chr17:17250190-17250190 | p.R208fs*>21 | 1 |
chr17:17209944-17209944 | p.A119T | 1 |
chr17:17250190-17250191 | p.R208fs*>22 | 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 | 3 |   |   | 1 |   | 2 |   |   | 2 |   |   |   | 1 | 3 | 2 |   | 4 |
# mutation |   | 1 | 1 | 3 |   |   | 1 |   | 2 |   |   | 2 |   |   |   | 1 | 3 | 2 |   | 4 |
nonsynonymous SNV |   |   |   | 2 |   |   |   |   | 2 |   |   | 1 |   |   |   |   | 2 |   |   | 3 |
synonymous SNV |   | 1 | 1 | 1 |   |   | 1 |   |   |   |   | 1 |   |   |   | 1 | 1 | 2 |   | 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 |
chr17:17209886 | p.D217N | 1 |
chr17:17250123 | p.K99N | 1 |
chr17:17209911 | p.P227L | 1 |
chr17:17250164 | p.L108L | 1 |
chr17:17209922 | p.A111A | 1 |
chr17:17250185 | p.V115V | 1 |
chr17:17209934 | p.C129F | 1 |
chr17:17250213 | p.P132R | 1 |
chr17:17226516 | p.P153S | 1 |
chr17:17250219 | p.V168V | 1 |
Other DBs for Point Mutations |
Copy Number for NT5M 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 NT5M |
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 |
ATPAF2,LAMTOR4,CLPP,COPS3,CUEDC2,MZT2B,FAM195A, FIS1,NAA38,MED9,MYL5,LRRC75A-AS1,NT5M,PEMT, PLD6,QTRT1,RANGRF,RNASEK,SAT2,VPS37D,ZSWIM7 | AARSD1,ATG4D,ATP5D,ATP5SL,DVL1,ECSIT,FAM195A, KLHDC3,LRRC47,MACROD1,MRPL14,MRPL38,NDUFA7,NDUFV1, NT5M,PACSIN3,PTGES2,STK25,TBRG4,TMEM201,TRAP1 | ||||
ALOX12B,C17orf49,DVL2,GLS2,HAUS4,HTRA2,KLHL35, LOC284023,MED9,LRRC75A-AS1,NPB,NT5M,PEMT,PKN3, PLD6,PRPSAP2,SLC25A11,TMEM231,UBB,ZNF232,ZSWIM7 | ANGPTL1,APBB1,TMEM240,PIFO,C3orf18,FAXC,DIXDC1, ENOX1,FBXO17,ARHGEF25,HSPB8,ILK,LMO3,NECAB1, NT5M,PDZRN4,REEP1,SOX15,SSPN,TMEM35,TSPAN2 |
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 NT5M |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00987 | 5',3'-nucleotidase, mitochondrial | approved; investigational | Cytarabine | ||
DB02745 | 5',3'-nucleotidase, mitochondrial | experimental | Uridine |
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Cross referenced IDs for NT5M |
* 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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