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 NME2
Basic gene info.Gene symbolNME2
Gene nameNME/NM23 nucleoside diphosphate kinase 2
SynonymsNDKB|NDPK-B|NDPKB|NM23-H2|NM23B|PUF
CytomapUCSC genome browser: 17q21.3
Genomic locationchr17 :49242795-49249105
Type of geneprotein-coding
RefGenesNM_001018137.2,
NM_001018138.1,NM_001018139.2,NM_001198682.1,NM_002512.3,
Ensembl idENSG00000011052
DescriptionHEL-S-155anNDP kinase Bc-myc purine-binding transcription factor PUFc-myc transcription factorepididymis secretory sperm binding protein Li 155anhistidine protein kinase NDKBnon-metastatic cells 2, protein (NM23) expressed innon-metastatic cells 2,
Modification date20141222
dbXrefs MIM : 156491
HGNC : HGNC
Ensembl : ENSG00000011052
Ensembl : ENSG00000243678
HPRD : 01132
Vega : OTTHUMG00000154062
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NME2
BioGPS: 4831
Gene Expression Atlas: ENSG00000011052
The Human Protein Atlas: ENSG00000011052
PathwayNCI Pathway Interaction Database: NME2
KEGG: NME2
REACTOME: NME2
ConsensusPathDB
Pathway Commons: NME2
MetabolismMetaCyc: NME2
HUMANCyc: NME2
RegulationEnsembl's Regulation: ENSG00000011052
miRBase: chr17 :49,242,795-49,249,105
TargetScan: NM_001018137
cisRED: ENSG00000011052
ContextiHOP: NME2
cancer metabolism search in PubMed: NME2
UCL Cancer Institute: NME2
Assigned class in ccmGDBC

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Phenotypic Information for NME2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NME2
Familial Cancer Database: NME2
* 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
Orphanet
DiseaseKEGG Disease: NME2
MedGen: NME2 (Human Medical Genetics with Condition)
ClinVar: NME2
PhenotypeMGI: NME2 (International Mouse Phenotyping Consortium)
PhenomicDB: NME2

Mutations for NME2
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 NME2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
EC440105RPL27148174115080141150848NME24496174924560849245660
EC572330RPL27551174115080241150848NME24799174924560849245660
AW964262NME21287174924624249246528MAGI128270636576343465763857
FJ655906RPL2711345174115076041154765NME2345395174924888249248932
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 # sample2               1
GAIN (# sample)2               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=3)
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
chr17:49247316-49247316p.V83M2
chr17:49248846-49248846p.?1
chr17:49244193-49244193p.M1T1
chr17:49248891-49248891p.E129*1
chr17:49244208-49244208p.R6L1
chr17:49248918-49248918p.E138*1
chr17:49245615-49245615p.H47N1
chr17:49248942-49248942p.A146S1
chr17:49245626-49245626p.Q50Q1
chr17:49248943-49248943p.A146V1

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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=0

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample                    
# mutation                    
nonsynonymous SNV                    
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

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 NME2 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 NME2

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

ABCC3,ATP5G1,LBX2,LRRC59,LUC7L3,MRPL27,NME1,
NME1-NME2,NME2,NME2P1,NUDT8,PHB,RSAD1,RTL1,
SLC12A3,SLC35B1,SNF8,SPAG9,STRA13,TOB1,UTP18
APRT,C12orf10,CNPY2,EEF1D,EIF3G,FAU,NHP2,
NME2,NSMCE1,RPL13,RPL18,RPL19,RPL27A,RPL35,
RPL36,RPL7A,RPL8,RPS15,RPS9,SLC27A5,SNRPD2

ANAPC11,ATP5G1,ATP5H,C17orf89,COA3,ICT1,MRPL12,
MRPL27,MRPS23,MRPS7,NME1,NME2,PHB,PSMB3,
RPL27,RPL38,SLC25A39,SNRPD2,TACO1,UTP18,ZNHIT3
BNIP1,BOLA3,TMEM258,C1QBP,TMEM261,EBNA1BP2,LSM2,
MRPL11,MRPL52,MRPS7,NHP2,NME2,NPM3,POLR1C,
PRDX4,RPSAP58,SF3B5,SNRNP40,SNRPB,SNRPD2,TOMM6
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 NME2
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
DB04315NME/NM23 nucleoside diphosphate kinase 2experimentalGuanosine-5'-Diphosphate
DB00709NME/NM23 nucleoside diphosphate kinase 2approved; investigationalLamivudine
DB00171NME/NM23 nucleoside diphosphate kinase 2approved; nutraceuticalAdenosine triphosphate
DB00495NME/NM23 nucleoside diphosphate kinase 2approvedZidovudine
DB00544NME/NM23 nucleoside diphosphate kinase 2approvedFluorouracil
DB00130NME/NM23 nucleoside diphosphate kinase 2approved; nutraceutical; investigationalL-Glutamine


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Cross referenced IDs for NME2
* 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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