Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 NT5C
Basic gene info.Gene symbolNT5C
Gene name5', 3'-nucleotidase, cytosolic
SynonymsDNT|DNT1|HEL74|P5N2|PN-I|PN-II|UMPH2|cdN|dNT-1
CytomapUCSC genome browser: 17q25.1
Genomic locationchr17 :73126319-73127890
Type of geneprotein-coding
RefGenesNM_001252377.1,
NM_014595.2,NR_045513.1,
Ensembl idENSG00000125458
Description5' nucleotidase, deoxy (pyrimidine), cytosolic type C5'(3')-deoxyribonucleotidase, cytosolic typecytosolic 5',3'-pyrimidine nucleotidasedeoxy-5'-nucleotidase 1epididymis luminal protein 74uridine 5'-monophosphate phosphohydrolase 2uridine 5-prime mo
Modification date20141207
dbXrefs MIM : 191720
HGNC : HGNC
Ensembl : ENSG00000125458
HPRD : 11833
Vega : OTTHUMG00000179346
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NT5C
BioGPS: 30833
Gene Expression Atlas: ENSG00000125458
The Human Protein Atlas: ENSG00000125458
PathwayNCI Pathway Interaction Database: NT5C
KEGG: NT5C
REACTOME: NT5C
ConsensusPathDB
Pathway Commons: NT5C
MetabolismMetaCyc: NT5C
HUMANCyc: NT5C
RegulationEnsembl's Regulation: ENSG00000125458
miRBase: chr17 :73,126,319-73,127,890
TargetScan: NM_001252377
cisRED: ENSG00000125458
ContextiHOP: NT5C
cancer metabolism search in PubMed: NT5C
UCL Cancer Institute: NT5C
Assigned class in ccmGDBC

Top
Phenotypic Information for NT5C(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NT5C
Familial Cancer Database: NT5C
* 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_PURINE_METABOLISM
REACTOME_PYRIMIDINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NT5C
MedGen: NT5C (Human Medical Genetics with Condition)
ClinVar: NT5C
PhenotypeMGI: NT5C (International Mouse Phenotyping Consortium)
PhenomicDB: NT5C

Mutations for NT5C
* 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
ovaryNT5Cchr177312711273127132HN1chr177313582173135841
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 NT5C 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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=6)
Stat. for Synonymous SNVs
(# total SNVs=1)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr17:73126909-73126909p.L130L2
chr17:73126884-73126884p.G139W2
chr17:73127325-73127325p.P76S1
chr17:73127332-73127332p.D73D1
chr17:73127348-73127348p.P68R1
chr17:73127364-73127364p.S63R1
chr17:73127683-73127683p.Q40Q1
chr17:73126663-73126663p.T176A1
chr17:73126675-73126675p.V172F1
chr17:73126904-73126904p.R132M1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   1  1          1 1
# mutation   1  1          1 1
nonsynonymous SNV   1             1 1
synonymous SNV      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])

Top
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
chr17:73127325p.V61V,NT5C1
chr17:73127368p.T136A,NT5C1
chr17:73126663p.V132F,NT5C1
chr17:73126675p.T124N,NT5C1
chr17:73126698p.R132M1
chr17:73126904p.P76S,NT5C1

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 NT5C 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]

Top
Gene Expression for NT5C

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

CBX3,CMPK2,CYCS,DDX58,HESX1,IFI44,IFI44L,
IFIH1,IFIT1,IFIT2,IFIT3,IFNB1,MX2,NT5C3A,
OAS2,OASL,PARP12,RSAD2,SAMD9L,USP18,XAF1
BRMS1L,SPRYD7,FAM210A,COX11,E2F6,EIF3J,HSF2,
MMADHC,MOB4,NDUFA5,NT5C3A,PPP1CB,PPP1R2,PRKRA,
RAB12,RFESD,RWDD4,UBE2B,VBP1,VTA1,YAF2

ARL4A,C1GALT1,MALSU1,CBX3,CCT6A,CYCS,GARS,
GGCT,GLRX2,HUS1,LSM5,MRPL32,NT5C3A,PRSS3,
PSMA2,RAC1,RALA,RP9P,S100A10,SEC61G,TAX1BP1
ARPC2,CAP1,CASP10,CASP3,CASP7,CASP8,CCDC68,
CEACAM1,CEACAM6,CLIC5,HPSE,KRT20,MAPK6,MYD88,
NT5C3A,OSTF1,PLAC8,RALB,RNF19B,TDRD7,TPM3
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for NT5C
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, cytosolicapproved; investigationalCytarabine
DB007095', 3'-nucleotidase, cytosolicapproved; investigationalLamivudine
DB027455', 3'-nucleotidase, cytosolicexperimentalUridine
DB005445', 3'-nucleotidase, cytosolicapprovedFluorouracil


Top
Cross referenced IDs for NT5C
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas