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 NME1

Basic gene info.	Gene symbol	NME1
	Gene name	NME/NM23 nucleoside diphosphate kinase 1
	Synonyms	AWD\|GAAD\|NB\|NBS\|NDKA\|NDPK-A\|NDPKA\|NM23\|NM23-H1
	Cytomap	UCSC genome browser: 17q21.3
	Genomic location	chr17 :49230919-49239450
	Type of gene	protein-coding
	RefGenes	NM_000269.2, NM_198175.1,
	Ensembl id	ENSG00000239672
	Description	NDP kinase Agranzyme A-activated DNasemetastasis inhibition factor nm23non-metastatic cells 1, protein (NM23A) expressed innucleoside diphosphate kinase Atumor metastatic process-associated protein
	Modification date	20141207
dbXrefs	MIM : 156490
	HGNC : HGNC
	Ensembl : ENSG00000239672
	HPRD : 01131
	Vega : OTTHUMG00000137474
Protein	UniProt: P15531 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NME1
	BioGPS: 4830
	Gene Expression Atlas: ENSG00000239672
	The Human Protein Atlas: ENSG00000239672
Pathway	NCI Pathway Interaction Database: NME1
	KEGG: NME1
	REACTOME: NME1
	ConsensusPathDB
	Pathway Commons: NME1
Metabolism	MetaCyc: NME1
	HUMANCyc: NME1
Regulation	Ensembl's Regulation: ENSG00000239672
	miRBase: chr17 :49,230,919-49,239,450
	TargetScan: NM_000269
	cisRED: ENSG00000239672
Context	iHOP: NME1
	cancer metabolism search in PubMed: NME1
	UCL Cancer Institute: NME1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NME1 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_PURINE_METABOLISM KEGG_PYRIMIDINE_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES

Others
OMIM	156490; gene.
Orphanet
Disease	KEGG Disease: NME1
	MedGen: NME1 (Human Medical Genetics with Condition)
	ClinVar: NME1
Phenotype	MGI: NME1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NME1 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
BF762367	NME1	42	125	17	49239270	49239353	LRP5	121	388	11	68183863	68191091
BE765003	NME1	12	143	17	49230965	49233086	THRA	135	205	17	38246322	38246392
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=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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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
chr17:49233063-49233063	p.V41V	1
chr17:49239159-49239159	p.E163K	1
chr17:49233106-49233106	p.K56E	1
chr17:49239204-49239204	p.*178R	1
chr17:49237347-49237347	p.E70K	1
chr17:49237348-49237348	p.E70A	1
chr17:49237379-49237379	p.L80L	1
chr17:49237387-49237387	p.R83H	1
chr17:49237425-49237425	p.G96W	1
chr17:49238549-49238549	p.T111M	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=1

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				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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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
chr17:49231764	p.V10V	1
chr17:49239125	p.A126A,NME1	1
chr17:49239140	p.G131G,NME1	1

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 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

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


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

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 NME1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL2159; -.
Organism-specific databases	PharmGKB	PA249; -.
Organism-specific databases	CTD	4830; -.

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
DB02181	NME/NM23 nucleoside diphosphate kinase 1	experimental	2'-Deoxyguanosine-5'-Triphosphate
DB02212	NME/NM23 nucleoside diphosphate kinase 1	experimental	Pyrophosphate 2-
DB02345	NME/NM23 nucleoside diphosphate kinase 1	experimental	Selenocysteine
DB02569	NME/NM23 nucleoside diphosphate kinase 1	experimental	2',3'-Dehydro-2',3'-Deoxy-Thymidine 5'-Diphosphate
DB02607	NME/NM23 nucleoside diphosphate kinase 1	experimental	Adenosine Phosphonoacetic Acid
DB02887	NME/NM23 nucleoside diphosphate kinase 1	experimental	2',3'-Dehydro-2',3'-Deoxy-Thymidine 5'-Triphosphate
DB03103	NME/NM23 nucleoside diphosphate kinase 1	experimental	Thymidine-5'- Diphosphate
DB03431	NME/NM23 nucleoside diphosphate kinase 1	experimental	Adenosine-5'-Diphosphate
DB03491	NME/NM23 nucleoside diphosphate kinase 1	experimental	2'-Deoxyguanosine-5'-Diphosphate
DB04068	NME/NM23 nucleoside diphosphate kinase 1	experimental	Fudp
DB04315	NME/NM23 nucleoside diphosphate kinase 1	experimental	Guanosine-5'-Diphosphate
DB04366	NME/NM23 nucleoside diphosphate kinase 1	experimental	3'-Deoxy 3'-Amino Adenosine-5'-Diphosphate
DB04542	NME/NM23 nucleoside diphosphate kinase 1	experimental	3'-Azido-3'-Deoxythymidine-5'-Diphosphate
DB00709	NME/NM23 nucleoside diphosphate kinase 1	approved; investigational	Lamivudine
DB00171	NME/NM23 nucleoside diphosphate kinase 1	approved; nutraceutical	Adenosine triphosphate
DB00495	NME/NM23 nucleoside diphosphate kinase 1	approved	Zidovudine
DB00544	NME/NM23 nucleoside diphosphate kinase 1	approved	Fluorouracil
DB00122	NME/NM23 nucleoside diphosphate kinase 1	approved; nutraceutical	Choline
DB00130	NME/NM23 nucleoside diphosphate kinase 1	approved; nutraceutical; investigational	L-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