Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 NME5
Basic gene info.Gene symbolNME5
Gene nameNME/NM23 family member 5
SynonymsNM23-H5|NM23H5|RSPH23
CytomapUCSC genome browser: 5q31
Genomic locationchr5 :137450860-137475132
Type of geneprotein-coding
RefGenesNM_003551.2,
Ensembl idENSG00000112981
DescriptionIPIA-betaNDK-H 5NDP kinase homolog 5inhibitor of p53-induced apoptosis-betanon-metastatic cells 5, protein expressed in (nucleoside-diphosphate kinase)nucleoside diphosphate kinase homolog 5radial spoke 23 homologtestis-specific nm23 homolog
Modification date20141207
dbXrefs MIM : 603575
HGNC : HGNC
Ensembl : ENSG00000112981
HPRD : 04655
Vega : OTTHUMG00000129207
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NME5
BioGPS: 8382
Gene Expression Atlas: ENSG00000112981
The Human Protein Atlas: ENSG00000112981
PathwayNCI Pathway Interaction Database: NME5
KEGG: NME5
REACTOME: NME5
ConsensusPathDB
Pathway Commons: NME5
MetabolismMetaCyc: NME5
HUMANCyc: NME5
RegulationEnsembl's Regulation: ENSG00000112981
miRBase: chr5 :137,450,860-137,475,132
TargetScan: NM_003551
cisRED: ENSG00000112981
ContextiHOP: NME5
cancer metabolism search in PubMed: NME5
UCL Cancer Institute: NME5
Assigned class in ccmGDBC

Top
Phenotypic Information for NME5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NME5
Familial Cancer Database: NME5
* 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: NME5
MedGen: NME5 (Human Medical Genetics with Condition)
ClinVar: NME5
PhenotypeMGI: NME5 (International Mouse Phenotyping Consortium)
PhenomicDB: NME5

Mutations for NME5
* 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
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryNME5chr5137469153137469173NME5chr5137456864137456884
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 NME5 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

Top
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.

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=8)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

Top
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
chr5:137474391-137474391p.E27K2
chr5:137454523-137454523p.K180T2
chr5:137474445-137474445p.Q9*2
chr5:137451406-137451406p.K201fs*82
chr5:137451461-137451461p.?1
chr5:137474385-137474385p.E29*1
chr5:137454515-137454515p.D183Y1
chr5:137474399-137474399p.V24A1
chr5:137454564-137454565p.M166fs*61
chr5:137474402-137474402p.I23S1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  1    1  2     4 1
# mutation1  1    1  2     3 1
nonsynonymous SNV1  1    1  2     2 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])

Top
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
chr5:137474391p.E27K2
chr5:137454523p.K180T2
chr5:137454576p.N162K1
chr5:137465150p.K46I1
chr5:137474373p.I33V1
chr5:137474399p.V24A1
chr5:137454515p.D183Y1
chr5:137454573p.L163L1

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 NME5 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]

Top
Gene Expression for NME5

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

CFAP43,C2orf73,C9orf116,AK8,CASC1,CASC2,CFAP53,
CCDC65,LRRC48,NME5,NPHP1,OSCP1,PIH1D2,RIBC1,
RSPH1,SPATA4,SPEF2,TCTN1,TMEM232,WDR78,ZMYND10
ADSS,BUB3,VWA9,CDK7,CDS1,DYX1C1,EEF1E1,
ENPP5,FBXO16,HMGN1,IFT88,IQCK,KIAA0895,LCA5L,
MYCBP,NME5,PPA2,RBM11,SPATA17,TTC19,TTC8

KIAA0825,TRAPPC13,COX11,FBXL5,IDH1,IRAK1BP1,MDH1B,
MOCS2,NME5,NPHP1,NRADDP,NSL1,OR4F15,PIH1D2,
SNAPIN,SP8,SRP9,TTC1,TXNDC9,UBA3,YAF2
TMEM237,ASB5,B3GALNT1,CCDC169,FAM229B,CFAP36,MICU3,
EIF5A2,FGF10,FKBP7,FXYD1,GNG11,HDGFRP3,KIAA0895,
LOH12CR2,NME4,NME5,PTN,SNCA,TCEAL1,TPD52L1
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for NME5


There's no related Drug.
Top
Cross referenced IDs for NME5
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas