Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 NT5C2
Basic gene info.Gene symbolNT5C2
Gene name5'-nucleotidase, cytosolic II
SynonymsGMP|NT5B|PNT5|SPG45|SPG65|cN-II
CytomapUCSC genome browser: 10q24.32
Genomic locationchr10 :104847773-104953063
Type of geneprotein-coding
RefGenesNM_001134373.2,
NM_012229.4,
Ensembl idENSG00000076685
Description5'-nucleotidase (purine), cytosolic type BIMP-specific 5'-NTcytosolic 5'-nucleotidase IIcytosolic purine 5'-nucleotidasepurine 5' nucleotidase
Modification date20141207
dbXrefs MIM : 600417
HGNC : HGNC
Ensembl : ENSG00000076685
HPRD : 02686
Vega : OTTHUMG00000018981
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NT5C2
BioGPS: 22978
Gene Expression Atlas: ENSG00000076685
The Human Protein Atlas: ENSG00000076685
PathwayNCI Pathway Interaction Database: NT5C2
KEGG: NT5C2
REACTOME: NT5C2
ConsensusPathDB
Pathway Commons: NT5C2
MetabolismMetaCyc: NT5C2
HUMANCyc: NT5C2
RegulationEnsembl's Regulation: ENSG00000076685
miRBase: chr10 :104,847,773-104,953,063
TargetScan: NM_001134373
cisRED: ENSG00000076685
ContextiHOP: NT5C2
cancer metabolism search in PubMed: NT5C2
UCL Cancer Institute: NT5C2
Assigned class in ccmGDBC

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Phenotypic Information for NT5C2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NT5C2
Familial Cancer Database: NT5C2
* 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_ABACAVIR_TRANSPORT_AND_METABOLISM
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PURINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NT5C2
MedGen: NT5C2 (Human Medical Genetics with Condition)
ClinVar: NT5C2
PhenotypeMGI: NT5C2 (International Mouse Phenotyping Consortium)
PhenomicDB: NT5C2

Mutations for NT5C2
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NT5C2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE936930NT5C21213910104879475104879603NT5C213630310104878417104878583
BE936897NT5C2116910104879430104879603NT5C215736810104878404104878617
AW008648NT5C2113510104952890104953024NT5C212650510104952285104952664
BE178418NT5C2130510104879460104879765NT5C230161510104878246104878560
DA677984NT5C2128510104934614104953029SHOC228457910112723882112724177
BE178183NT5C21631910104878246104878557NT5C231563110104879448104879765

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               1
GAIN (# sample)                 
LOSS (# sample)1               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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=33)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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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
chr10:104934693-104934693p.R8Q3
chr10:104852955-104852955p.R367Q3
chr10:104859732-104859732p.R195Q2
chr10:104866378-104866378p.L87L2
chr10:104851364-104851364p.E390K2
chr10:104866428-104866428p.E71K2
chr10:104854184-104854184p.S281F2
chr10:104852972-104852972p.K361N1
chr10:104849497-104849497p.A540P1
chr10:104850701-104850701p.R422C1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2 1121      14  136 8
# mutation2 1131      14  137 10
nonsynonymous SNV2 18       14  137 7
synonymous SNV   51              3
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
chr10:104852955p.R367Q,NT5C23
chr10:104934693p.R195Q,NT5C22
chr10:104859732p.E390K,NT5C22
chr10:104851364p.R8Q,NT5C22
chr10:104859733p.R456C,NT5C21
chr10:104849519p.A451V,NT5C21
chr10:104934623p.R195W,NT5C21
chr10:104852930p.S443N,NT5C21
chr10:104859772p.E182K,NT5C21
chr10:104849581p.T179A,NT5C21

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 NT5C2 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 NT5C2

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

ATL2,B3GNT5,CCDC82,CCNJ,CREB3L2,EML4,AMER1,
FMNL2,JRKL,NT5C2,PADI2,PCGF6,PPRC1,SFT2D2,
SMNDC1,STK38,TAF5,TTLL4,USP6NL,XPNPEP1,YEATS2
ANK3,KANSL2,TRMT13,DYRK1A,FAM160A1,LOC100128640,MTRF1,
NAA25,NT5C2,PDE4B,PDE7A,PM20D2,PSTPIP2,RTF1,
THAP9,TIAM2,TPP2,USP28,ZBTB43,ZC3H8,ZKSCAN5

ATAD1,BTRC,R3HCC1L,C10orf76,CPEB3,EXOC6,HERC4,
LIPH,MARCH5,MGEA5,MXI1,MYOF,NT5C2,PLCE1,
SEMA4G,SHOC2,SLC17A5,SLK,TBC1D12,TCF7L2,TM9SF3
ABHD3,ACER3,ACTR2,AHCYL2,B4GALT1,CEACAM1,DHRS9,
FAM126B,FEM1C,GPD2,ITCH,MAPRE3,MIER3,NT5C2,
RBM47,RNF6,SLC26A3,TMEM65,TMPRSS2,XIAP,YWHAB
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 NT5C2
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
DB001715'-nucleotidase, cytosolic IIapproved; nutraceuticalAdenosine triphosphate
DB008115'-nucleotidase, cytosolic IIapprovedRibavirin
DB001735'-nucleotidase, cytosolic IIapproved; nutraceuticalAdenine
DB005155'-nucleotidase, cytosolic IIapprovedCisplatin
DB004415'-nucleotidase, cytosolic IIapprovedGemcitabine
DB009875'-nucleotidase, cytosolic IIapproved; investigationalCytarabine
DB006405'-nucleotidase, cytosolic IIapproved; investigationalAdenosine


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Cross referenced IDs for NT5C2
* 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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