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 NME3
Basic gene info.Gene symbolNME3
Gene nameNME/NM23 nucleoside diphosphate kinase 3
SynonymsDR-nm23|NDPK-C|NDPKC|NM23-H3|NM23H3|c371H6.2
CytomapUCSC genome browser: 16q13.3
Genomic locationchr16 :1820320-1821710
Type of geneprotein-coding
RefGenesNM_002513.2,
Ensembl idENSG00000103024
DescriptionNDK 3NDP kinase 3NDP kinase Cnon-metastatic cells 3, protein expressed innucleoside diphosphate kinase 3nucleoside diphosphate kinase C
Modification date20141207
dbXrefs MIM : 601817
HGNC : HGNC
Ensembl : ENSG00000103024
HPRD : 03488
Vega : OTTHUMG00000128635
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NME3
BioGPS: 4832
Gene Expression Atlas: ENSG00000103024
The Human Protein Atlas: ENSG00000103024
PathwayNCI Pathway Interaction Database: NME3
KEGG: NME3
REACTOME: NME3
ConsensusPathDB
Pathway Commons: NME3
MetabolismMetaCyc: NME3
HUMANCyc: NME3
RegulationEnsembl's Regulation: ENSG00000103024
miRBase: chr16 :1,820,320-1,821,710
TargetScan: NM_002513
cisRED: ENSG00000103024
ContextiHOP: NME3
cancer metabolism search in PubMed: NME3
UCL Cancer Institute: NME3
Assigned class in ccmGDBC

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Phenotypic Information for NME3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NME3
Familial Cancer Database: NME3
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NME3
MedGen: NME3 (Human Medical Genetics with Condition)
ClinVar: NME3
PhenotypeMGI: NME3 (International Mouse Phenotyping Consortium)
PhenomicDB: NME3

Mutations for NME3
* 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 NME3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA688018CTDSPL21737154473889544738915NME3282161618203211820511

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
There's no copy number variation information in COSMIC data for this gene.

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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=11

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=5)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr16:1820992-1820992p.V94V11
chr16:1821297-1821297p.A54V1
chr16:1820659-1820659p.L167L1
chr16:1821306-1821306p.K51R1
chr16:1820734-1820734p.S142R1
chr16:1821355-1821355p.R35W1
chr16:1820735-1820735p.S142N1
chr16:1821500-1821500p.L12L1
chr16:1820749-1820749p.S137S1
chr16:1820904-1820904p.D124Y1

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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        1   1   
# mutation   1        1   1   
nonsynonymous SNV   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])

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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
chr16:1820659p.L167L1
chr16:1820904p.D124Y1
chr16:1820909p.R122H1

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 NME3 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 NME3

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

C16orf13,TSR3,ECI1,FAM173A,FAM195A,FLYWCH2,METRN,
MPG,MRPL28,MRPS34,NARFL,NDUFB10,NME3,NUBP2,
PIGQ,RHOT2,SPSB3,STUB1,TCEB2,ZNF205,ZNF688
C1orf86,PPP1R35,C9orf142,DGCR6L,DPM3,MVB12A,MZT2B,
FBXL15,HSPBP1,MPG,NME3,NPDC1,NUBP2,PTRH1,
RAB11B,RBM42,SCAND1,SIRT6,SNAPC2,TMUB1,TRAPPC5

C16orf13,TSR3,CCS,ECI1,E4F1,FAM195A,FKBP2,
JMJD8,MLST8,MPG,MRPL28,MRPS34,NARFL,NDUFB10,
NME3,NTHL1,NUBP2,RHOT2,RNF208,STUB1,THAP3
ALKBH7,APBA3,ATP5G2,C16orf13,C19orf60,C9orf16,DHPS,
DRG2,FBXL15,GNPTG,HMG20B,INO80B,MPG,NDUFAF3,
NME3,RABAC1,RPL13,RPS15,TRAPPC5,UNC119,ZNF688
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 NME3


There's no related Drug.
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Cross referenced IDs for NME3
* 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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