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 NME1
Basic gene info.Gene symbolNME1
Gene nameNME/NM23 nucleoside diphosphate kinase 1
SynonymsAWD|GAAD|NB|NBS|NDKA|NDPK-A|NDPKA|NM23|NM23-H1
CytomapUCSC genome browser: 17q21.3
Genomic locationchr17 :49230919-49239450
Type of geneprotein-coding
RefGenesNM_000269.2,
NM_198175.1,
Ensembl idENSG00000239672
DescriptionNDP kinase Agranzyme A-activated DNasemetastasis inhibition factor nm23non-metastatic cells 1, protein (NM23A) expressed innucleoside diphosphate kinase Atumor metastatic process-associated protein
Modification date20141207
dbXrefs MIM : 156490
HGNC : HGNC
Ensembl : ENSG00000239672
HPRD : 01131
Vega : OTTHUMG00000137474
ProteinUniProt: P15531
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NME1
BioGPS: 4830
Gene Expression Atlas: ENSG00000239672
The Human Protein Atlas: ENSG00000239672
PathwayNCI Pathway Interaction Database: NME1
KEGG: NME1
REACTOME: NME1
ConsensusPathDB
Pathway Commons: NME1
MetabolismMetaCyc: NME1
HUMANCyc: NME1
RegulationEnsembl's Regulation: ENSG00000239672
miRBase: chr17 :49,230,919-49,239,450
TargetScan: NM_000269
cisRED: ENSG00000239672
ContextiHOP: NME1
cancer metabolism search in PubMed: NME1
UCL Cancer Institute: NME1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NME1 in cancer cell metabolism1. Matimba A, Li F, Livshits A, Cartwright CS, Scully S, et al. (2014) Thiopurine pharmacogenomics: association of SNPs with clinical response and functional validation of candidate genes. Pharmacogenomics 15: 433-447. go to article

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Phenotypic Information for NME1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NME1
Familial Cancer Database: NME1
* 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
REACTOME_METABOLISM_OF_NUCLEOTIDES

check002.gifOthers
OMIM 156490; gene.
Orphanet
DiseaseKEGG Disease: NME1
MedGen: NME1 (Human Medical Genetics with Condition)
ClinVar: NME1
PhenotypeMGI: NME1 (International Mouse Phenotyping Consortium)
PhenomicDB: NME1

Mutations for NME1
* 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 NME1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF762367NME142125174923927049239353LRP5121388116818386368191091
BE765003NME112143174923096549233086THRA135205173824632238246392
BC107894NME13594175115355951162089NME25951195175116543551171744
BC133029NME11375175115355951162089NME2376875175116543551171744
BC133031NME11375175115355951162089NME2376875175116543551171744

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)                 
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=7)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr17:49239125-49239125p.A151A1
chr17:49231768-49231768p.Q12*1
chr17:49239140-49239140p.G156G1
chr17:49233063-49233063p.V41V1
chr17:49239159-49239159p.E163K1
chr17:49233106-49233106p.K56E1
chr17:49239204-49239204p.*178R1
chr17:49237347-49237347p.E70K1
chr17:49237348-49237348p.E70A1
chr17:49237379-49237379p.L80L1

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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                    
synonymous SNV   1        1      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
chr17:49239140p.V10V1
chr17:49231764p.A126A,NME11
chr17:49239125p.G131G,NME11

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 NME1 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 NME1

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

AURKAIP1,C19orf70,CLPP,CUEDC2,EEF1D,MRPL27,MRPL54,
MYL6,NDUFA11,NDUFA13,NDUFS7,NME1,NME1-NME2,NME2,
NME2P1,NUDC,PIN1,SNF8,TIMM13,UQCR11,VPS28
ASNA1,EMC10,DNPH1,COPE,EXOSC4,FIBP,GIPC1,
HSPBP1,MPG,MPND,MRPS12,NHP2,NME1,NME1-NME2,
NUBP2,PHB,PPP4C,PTRH1,RUVBL2,TIMM13,TSTA3

ALG3,ATAD3B,BCL2L12,C16orf59,AUNIP,CCDC37,MRPL28,
MRTO4,NDUFS8,TONSL,NME1-NME2,NOC2L,NUDC,PKMYT1,
POLR3K,PSMB2,RECQL4,SLC4A9,SPO11,SRM,TUBG1
CLPB,EEF2KMT,FJX1,FXN,G6PC3,GTPBP4,HAUS7,
HM13,HSPBP1,LYAR,MLKL,MMP3,NME1-NME2,NOP2,
PA2G4,RIPK2,RUVBL1,SDF2L1,SRM,USP14,WDR4
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 NME1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2159; -.
Organism-specific databasesPharmGKB PA249; -.
Organism-specific databasesCTD 4830; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02181NME/NM23 nucleoside diphosphate kinase 1experimental2'-Deoxyguanosine-5'-Triphosphate
DB02212NME/NM23 nucleoside diphosphate kinase 1experimentalPyrophosphate 2-
DB02345NME/NM23 nucleoside diphosphate kinase 1experimentalSelenocysteine
DB02569NME/NM23 nucleoside diphosphate kinase 1experimental2',3'-Dehydro-2',3'-Deoxy-Thymidine 5'-Diphosphate
DB02607NME/NM23 nucleoside diphosphate kinase 1experimentalAdenosine Phosphonoacetic Acid
DB02887NME/NM23 nucleoside diphosphate kinase 1experimental2',3'-Dehydro-2',3'-Deoxy-Thymidine 5'-Triphosphate
DB03103NME/NM23 nucleoside diphosphate kinase 1experimentalThymidine-5'- Diphosphate
DB03431NME/NM23 nucleoside diphosphate kinase 1experimentalAdenosine-5'-Diphosphate
DB03491NME/NM23 nucleoside diphosphate kinase 1experimental2'-Deoxyguanosine-5'-Diphosphate
DB04068NME/NM23 nucleoside diphosphate kinase 1experimentalFudp
DB04315NME/NM23 nucleoside diphosphate kinase 1experimentalGuanosine-5'-Diphosphate
DB04366NME/NM23 nucleoside diphosphate kinase 1experimental3'-Deoxy 3'-Amino Adenosine-5'-Diphosphate
DB04542NME/NM23 nucleoside diphosphate kinase 1experimental3'-Azido-3'-Deoxythymidine-5'-Diphosphate
DB00709NME/NM23 nucleoside diphosphate kinase 1approved; investigationalLamivudine
DB00171NME/NM23 nucleoside diphosphate kinase 1approved; nutraceuticalAdenosine triphosphate
DB00495NME/NM23 nucleoside diphosphate kinase 1approvedZidovudine
DB00544NME/NM23 nucleoside diphosphate kinase 1approvedFluorouracil
DB00122NME/NM23 nucleoside diphosphate kinase 1approved; nutraceuticalCholine
DB00130NME/NM23 nucleoside diphosphate kinase 1approved; nutraceutical; investigationalL-Glutamine


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Cross referenced IDs for NME1
* 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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