Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 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)

Cancer 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/

Metabolic Pathway Description
KEGG_PURINE_METABOLISM KEGG_PYRIMIDINE_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES

Others
OMIM
Orphanet
Disease	KEGG Disease: NME2
	MedGen: NME2 (Human Medical Genetics with Condition)
	ClinVar: NME2
Phenotype	MGI: NME2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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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'.

- 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)

Related fusion transcripts : go to Chitars2.0

* 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

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr17:49247316-49247316	p.V83M	2
chr17:49248846-49248846	p.?	1
chr17:49244193-49244193	p.M1T	1
chr17:49248891-49248891	p.E129*	1
chr17:49244208-49244208	p.R6L	1
chr17:49248918-49248918	p.E138*	1
chr17:49245615-49245615	p.H47N	1
chr17:49248942-49248942	p.A146S	1
chr17:49245626-49245626	p.Q50Q	1
chr17:49248943-49248943	p.A146V	1

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SNV 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 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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Top 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 Position

Mutation(aa)

Unique sampleID count

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* 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

: Open all cross reference information