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 NME7

Basic gene info.	Gene symbol	NME7
	Gene name	NME/NM23 family member 7
	Synonyms	CFAP67\|MN23H7\|NDK 7\|NDK7\|nm23-H7
	Cytomap	UCSC genome browser: 1q24
	Genomic location	chr1 :169101768-169337186
	Type of gene	protein-coding
	RefGenes	NM_013330.4, NM_197972.2,NR_104229.1,
	Ensembl id	ENSG00000143156
	Description	NDP kinase 7cilia and flagella associated protein 67non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)nucleoside diphosphate kinase 7nucleoside-diphosphate kinase 7
	Modification date	20141207
dbXrefs	MIM : 613465
	HGNC : HGNC
	Ensembl : ENSG00000143156
	HPRD : 11394
	Vega : OTTHUMG00000034586
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NME7
	BioGPS: 29922
	Gene Expression Atlas: ENSG00000143156
	The Human Protein Atlas: ENSG00000143156
Pathway	NCI Pathway Interaction Database: NME7
	KEGG: NME7
	REACTOME: NME7
	ConsensusPathDB
	Pathway Commons: NME7
Metabolism	MetaCyc: NME7
	HUMANCyc: NME7
Regulation	Ensembl's Regulation: ENSG00000143156
	miRBase: chr1 :169,101,768-169,337,186
	TargetScan: NM_013330
	cisRED: ENSG00000143156
Context	iHOP: NME7
	cancer metabolism search in PubMed: NME7
	UCL Cancer Institute: NME7
Assigned class in ccmGDB	C

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Phenotypic Information for NME7(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: NME7
	Familial Cancer Database: NME7

* 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

Others
OMIM
Orphanet
Disease	KEGG Disease: NME7
	MedGen: NME7 (Human Medical Genetics with Condition)
	ClinVar: NME7
Phenotype	MGI: NME7 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: NME7

Mutations for NME7

* 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

* 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	NME7	chr1	169297690	169297690	NME7	chr1	169312732	169312732
ovary	NME7	chr1	169328756	169328776		chr1	168515733	168515753
pancreas	NME7	chr1	169144761	169144781		chr11	26181598	26181618
pancreas	NME7	chr1	169145846	169145866		chr12	55733395	55733415
pancreas	NME7	chr1	169147327	169147347		chr3	35951527	35951547
pancreas	NME7	chr1	169160010	169160030	NME7	chr1	169160340	169160360
pancreas	NME7	chr1	169256766	169256786		chr12	40995235	40995255

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 NME7 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
BF913184	ZNF672	18	218	1	249143334	249145545	NME7	215	425	1	169308938	169309148
CA433037	RBM3	18	215	X	48436476	48436672	NME7	211	628	1	169102012	169336975

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	1		2		1				5					1	1	1	1
GAIN (# sample)	1		2						5					1	1	1	1
LOSS (# sample)					1				1

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=36)	Stat. for Synonymous SNVs (# total SNVs=2)

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
chr1:169267823-169267823	p.G207S	3
chr1:169293678-169293678	p.R22*	2
chr1:169256604-169256604	p.A231T	2
chr1:169267804-169267804	p.S213F	2
chr1:169102065-169102065	p.?	2
chr1:169199982-169199982	p.R322*	2
chr1:169267888-169267888	p.R185H	2
chr1:169293677-169293677	p.R22Q	1
chr1:169204413-169204413	p.E282Q	1
chr1:169267898-169267898	p.G182*	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=3

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	4		8	4		2		1	1		5	2				3	4		2
# mutation	1	4		6	4		2		1	1		8	3				3	4		2
nonsynonymous SNV	1	4		6	4		2		1	1		6	3				3	2		2
synonymous SNV												2						2

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
chr1:169267823	p.G207S,NME7	3
chr1:169256604	p.R185H,NME7	2
chr1:169267888	p.A231T,NME7	2
chr1:169256557	p.A212V,NME7	1
chr1:169267893	p.V68V,NME7	1
chr1:169292459	p.S210Y,NME7	1
chr1:169267909	p.E58D,NME7	1
chr1:169292473	p.P208H,NME7	1
chr1:169256627	p.N54Y,NME7	1
chr1:169267912	p.G207D,NME7	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 NME7 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 NME7

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


BLZF1,SAMD15,METTL18,TRMT1L,C1orf27,FAM229B,COG2, KIFAP3,MDH1B,MR1,MRPS14,NEK11,NME7,NPHP1, NSL1,PIH1D2,SCYL3,SNAPIN,TCTN2,VAMP4,XPR1	ALG2,PIFO,TMEM248,CETN2,DAZAP2,DDX47,IFT57, IQCK,LOC653566,MEAF6,NME7,PIGC,PPT1,IFT22, SLC35A1,SMU1,TCTN1,TCTN3,TMCO1,YWHAQ,ZDHHC6

TRMT1L,SWT1,CREG1,DEDD,NME7,PIP5K1A,POLR3C, PPOX,PRUNE,RBM8A,RNF2,SDCCAG8,SNAPIN,TIPRL, TOR1AIP1,TROVE2,TSNAX,UBE2Q1,UFC1,VPS45,VPS72	AP1S2,BBS10,BEX4,BMI1,C11orf74,C1orf123,C22orf39, CAMK1,CETN2,DNAJC18,EID1,FKBP7,MSANTD4,NGFRAP1, NKIRAS1,NME7,PABPC5,IFT22,RPL23AP82,TCEAL1,ZFP1

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 NME7

There's no related Drug.

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Cross referenced IDs for NME7

* 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