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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for NME2 |
Basic gene info. | Gene symbol | NME2 |
Gene name | NME/NM23 nucleoside diphosphate kinase 2 | |
Synonyms | NDKB|NDPK-B|NDPKB|NM23-H2|NM23B|PUF | |
Cytomap | UCSC genome browser: 17q21.3 | |
Genomic location | chr17 :49242795-49249105 | |
Type of gene | protein-coding | |
RefGenes | NM_001018137.2, NM_001018138.1,NM_001018139.2,NM_001198682.1,NM_002512.3, | |
Ensembl id | ENSG00000011052 | |
Description | HEL-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 date | 20141222 | |
dbXrefs | MIM : 156491 | |
HGNC : HGNC | ||
Ensembl : ENSG00000011052 | ||
Ensembl : ENSG00000243678 | ||
HPRD : 01132 | ||
Vega : OTTHUMG00000154062 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_NME2 | |
BioGPS: 4831 | ||
Gene Expression Atlas: ENSG00000011052 | ||
The Human Protein Atlas: ENSG00000011052 | ||
Pathway | NCI Pathway Interaction Database: NME2 | |
KEGG: NME2 | ||
REACTOME: NME2 | ||
ConsensusPathDB | ||
Pathway Commons: NME2 | ||
Metabolism | MetaCyc: NME2 | |
HUMANCyc: NME2 | ||
Regulation | Ensembl's Regulation: ENSG00000011052 | |
miRBase: chr17 :49,242,795-49,249,105 | ||
TargetScan: NM_001018137 | ||
cisRED: ENSG00000011052 | ||
Context | iHOP: NME2 | |
cancer metabolism search in PubMed: NME2 | ||
UCL Cancer Institute: NME2 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for NME2(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: NME2 |
Familial Cancer Database: NME2 |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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/ |
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KEGG_PURINE_METABOLISM KEGG_PYRIMIDINE_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: NME2 |
MedGen: NME2 (Human Medical Genetics with Condition) | |
ClinVar: NME2 | |
Phenotype | MGI: 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. |
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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
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- For Intra-chromosomal Variations |
There's no intra-chromosomal structural variation. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NME2 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
EC440105 | RPL27 | 1 | 48 | 17 | 41150801 | 41150848 | NME2 | 44 | 96 | 17 | 49245608 | 49245660 | |
EC572330 | RPL27 | 5 | 51 | 17 | 41150802 | 41150848 | NME2 | 47 | 99 | 17 | 49245608 | 49245660 | |
AW964262 | NME2 | 1 | 287 | 17 | 49246242 | 49246528 | MAGI1 | 282 | 706 | 3 | 65763434 | 65763857 | |
FJ655906 | RPL27 | 11 | 345 | 17 | 41150760 | 41154765 | NME2 | 345 | 395 | 17 | 49248882 | 49248932 | |
BC107894 | NME1 | 3 | 594 | 17 | 51153559 | 51162089 | NME2 | 595 | 1195 | 17 | 51165435 | 51171744 | |
BC133029 | NME1 | 1 | 375 | 17 | 51153559 | 51162089 | NME2 | 376 | 875 | 17 | 51165435 | 51171744 | |
BC133031 | NME1 | 1 | 375 | 17 | 51153559 | 51162089 | NME2 | 376 | 875 | 17 | 51165435 | 51171744 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 2 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 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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Stat. for Non-Synonymous SNVs (# total SNVs=7) | (# total SNVs=3) |
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(# total SNVs=0) | (# total SNVs=0) |
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* 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 position | Mutation(aa) | Unique sampleID count |
chr17:49247316-49247316 | p.V83M | 2 |
chr17:49245626-49245626 | p.Q50Q | 1 |
chr17:49248943-49248943 | p.A146V | 1 |
chr17:49245649-49245649 | p.R58Q | 1 |
chr17:49245686-49245686 | p.S70S | 1 |
chr17:49247298-49247298 | p.V77I | 1 |
chr17:49247315-49247315 | p.N82N | 1 |
chr17:49247383-49247383 | p.R105H | 1 |
chr17:49248846-49248846 | p.? | 1 |
chr17:49244193-49244193 | p.M1T | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# 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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* 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 Position | Mutation(aa) | Unique sampleID count |
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* 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. |
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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 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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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 | ||||
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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 |
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* 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 |
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Pharmacological Information for NME2 |
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DB Category | DB Name | DB's ID and Url link |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB04315 | NME/NM23 nucleoside diphosphate kinase 2 | experimental | Guanosine-5'-Diphosphate | ![]() | ![]() |
DB00709 | NME/NM23 nucleoside diphosphate kinase 2 | approved; investigational | Lamivudine | ![]() | ![]() |
DB00171 | NME/NM23 nucleoside diphosphate kinase 2 | approved; nutraceutical | Adenosine triphosphate | ![]() | ![]() |
DB00495 | NME/NM23 nucleoside diphosphate kinase 2 | approved | Zidovudine | ![]() | ![]() |
DB00544 | NME/NM23 nucleoside diphosphate kinase 2 | approved | Fluorouracil | ![]() | ![]() |
DB00130 | NME/NM23 nucleoside diphosphate kinase 2 | approved; nutraceutical; investigational | L-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 |
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