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 NT5C1B
Basic gene info.Gene symbolNT5C1B
Gene name5'-nucleotidase, cytosolic IB
SynonymsAIRP|CN-IB|CN1B
CytomapUCSC genome browser: 2p24.2
Genomic locationchr2 :18744136-18770846
Type of geneprotein-coding
RefGenesNM_001002006.2,
NM_001199086.1,NM_001199087.1,NM_001199088.1,NM_033253.3,
Ensembl idENSG00000185013
Descriptionautoimmune infertility-related proteincytosolic 5'-nucleotidase 1B
Modification date20141207
dbXrefs MIM : 610526
HGNC : HGNC
Ensembl : ENSG00000185013
HPRD : 11405
Vega : OTTHUMG00000151765
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NT5C1B
BioGPS: 93034
Gene Expression Atlas: ENSG00000185013
The Human Protein Atlas: ENSG00000185013
PathwayNCI Pathway Interaction Database: NT5C1B
KEGG: NT5C1B
REACTOME: NT5C1B
ConsensusPathDB
Pathway Commons: NT5C1B
MetabolismMetaCyc: NT5C1B
HUMANCyc: NT5C1B
RegulationEnsembl's Regulation: ENSG00000185013
miRBase: chr2 :18,744,136-18,770,846
TargetScan: NM_001002006
cisRED: ENSG00000185013
ContextiHOP: NT5C1B
cancer metabolism search in PubMed: NT5C1B
UCL Cancer Institute: NT5C1B
Assigned class in ccmGDBC

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Phenotypic Information for NT5C1B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NT5C1B
Familial Cancer Database: NT5C1B
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NT5C1B
MedGen: NT5C1B (Human Medical Genetics with Condition)
ClinVar: NT5C1B
PhenotypeMGI: NT5C1B (International Mouse Phenotyping Consortium)
PhenomicDB: NT5C1B

Mutations for NT5C1B
* 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 NT5C1B 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 # sample 1               
GAIN (# sample) 1               
LOSS (# sample)                 
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=54)
Stat. for Synonymous SNVs
(# total SNVs=23)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr2:18765453-18765453p.R324R5
chr2:18745319-18745319p.R526W3
chr2:18765428-18765428p.E333K3
chr2:18768783-18768783p.R36C3
chr2:18745097-18745097p.A600T2
chr2:18764161-18764161p.R392W2
chr2:18745341-18745341p.K518K2
chr2:18765507-18765507p.N306N2
chr2:18765813-18765813p.Y290Y2
chr2:18765443-18765443p.E328K2

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample           1        
# mutation           1        
nonsynonymous SNV           1        
synonymous SNV                    
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
chr2:18768216p.T115K1

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 NT5C1B 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 NT5C1B

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

PRR26,CLEC18B,CLEC18C,CLPS,EFCAB10,GFRA3,GRK1,
GRXCR1,LOC157381,LOC339788,LOXHD1,NOBOX,NT5C1B,POM121L8P,
POU5F1B,PTX4,RYR2,TPD52L3,TSGA10IP,UBE2U,ZAR1L
VRTN,C1QTNF8,C7orf33,CHD5,CLPS,COL9A1,CPNE6,
DKFZP434H168,DRP2,GRK1,HBG2,ITLN1,KIF1A,MLC1,
MYH11,NKX2-3,NOBOX,NT5C1B,POU5F1B,SOST,ZFP42

C9orf163,FOXC2,HIST1H2AK,HIST1H4E,HSF4,LCE5A,LOC100272217,
LOC401052,LOC730101,LINC00115,NPW,NT5C1B,PPP1R3E,PRORSD1P,
PROZ,RAB26,RPL13AP17,SPAG8,USP20,ZNF248,ZNF594
ACOX3,ANKRD13A,FANCD2OS,ERC2-IT1,TMEM249,CRYBA4,CXorf22,
FLJ40330,IRF4,JSRP1,KLK8,KRT74,LOC643719,LOC723972,
LRRC14B,NT5C1B,OR56B4,PPIL3,SNORA25,TAS2R3,TRIM31
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 NT5C1B
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
DB006405'-nucleotidase, cytosolic IBapproved; investigationalAdenosine


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Cross referenced IDs for NT5C1B
* 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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