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 NT5M
Basic gene info.Gene symbolNT5M
Gene name5',3'-nucleotidase, mitochondrial
SynonymsdNT-2|dNT2|mdN
CytomapUCSC genome browser: 17p11.2
Genomic locationchr17 :17206679-17250977
Type of geneprotein-coding
RefGenesNM_020201.3,
Ensembl idENSG00000205309
Description5' nucleotidase, mitochondrial5'(3')-deoxyribonucleotidase, mitochondrial5(3)-deoxyribonucleotidasedeoxy-5'-nucleotidase 2mitochondrial 5' nucleotidase
Modification date20141207
dbXrefs MIM : 605292
HGNC : HGNC
Ensembl : ENSG00000205309
HPRD : 12009
Vega : OTTHUMG00000059277
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NT5M
BioGPS: 56953
Gene Expression Atlas: ENSG00000205309
The Human Protein Atlas: ENSG00000205309
PathwayNCI Pathway Interaction Database: NT5M
KEGG: NT5M
REACTOME: NT5M
ConsensusPathDB
Pathway Commons: NT5M
MetabolismMetaCyc: NT5M
HUMANCyc: NT5M
RegulationEnsembl's Regulation: ENSG00000205309
miRBase: chr17 :17,206,679-17,250,977
TargetScan: NM_020201
cisRED: ENSG00000205309
ContextiHOP: NT5M
cancer metabolism search in PubMed: NT5M
UCL Cancer Institute: NT5M
Assigned class in ccmGDBC

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Phenotypic Information for NT5M(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NT5M
Familial Cancer Database: NT5M
* 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_PYRIMIDINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NT5M
MedGen: NT5M (Human Medical Genetics with Condition)
ClinVar: NT5M
PhenotypeMGI: 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryNT5Mchr171721280417212824ULK2chr171969475519694775
ovaryNT5Mchr171722496417224984ULK2chr171973748919737509
pancreasNT5Mchr171720687717207077chr175404068254040882
prostateNT5Mchr171724327517243275PEMTchr171742814017428140
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NT5M related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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                
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=11)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr17:17209886-17209886p.K99N2
chr17:17250250-17250250p.R226W2
chr17:17207002-17207002p.L46L1
chr17:17248196-17248196p.L173P1
chr17:17250254-17250254p.P227L1
chr17:17209877-17209877p.W96C1
chr17:17248215-17248215p.D179D1
chr17:17248229-17248229p.?1
chr17:17209911-17209911p.L108L1
chr17:17250123-17250123p.A183A1

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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 113  1 2  2   132 4
# mutation 113  1 2  2   132 4
nonsynonymous SNV   2    2  1    2  3
synonymous SNV 111  1    1   112 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
chr17:17207002p.W96L1
chr17:17248196p.S213S1
chr17:17209876p.W96C1
chr17:17248203p.A215A1
chr17:17209877p.K99N1
chr17:17248215p.D217N1
chr17:17209886p.L108L1
chr17:17250123p.P227L1
chr17:17209911p.A111A1
chr17:17250164p.V115V1

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 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

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

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
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 NT5M
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
DB009875',3'-nucleotidase, mitochondrialapproved; investigationalCytarabine
DB027455',3'-nucleotidase, mitochondrialexperimentalUridine


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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

: Open all cross reference information



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