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 NAMPT

Basic gene info.	Gene symbol	NAMPT
	Gene name	nicotinamide phosphoribosyltransferase
	Synonyms	1110035O14Rik\|PBEF\|PBEF1\|VF\|VISFATIN
	Cytomap	UCSC genome browser: 7q22.3
	Genomic location	chr7 :105888731-105925638
	Type of gene	protein-coding
	RefGenes	NM_005746.2, NM_182790.1,
	Ensembl id	ENSG00000105835
	Description	NAmPRTasepre-B cell-enhancing factorpre-B-cell colony enhancing factor 1pre-B-cell colony-enhancing factor 1
	Modification date	20141222
dbXrefs	MIM : 608764
	HGNC : HGNC
	Ensembl : ENSG00000105835
	HPRD : 09938
	Vega : OTTHUMG00000140388
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NAMPT
	BioGPS: 10135
	Gene Expression Atlas: ENSG00000105835
	The Human Protein Atlas: ENSG00000105835
Pathway	NCI Pathway Interaction Database: NAMPT
	KEGG: NAMPT
	REACTOME: NAMPT
	ConsensusPathDB
	Pathway Commons: NAMPT
Metabolism	MetaCyc: NAMPT
	HUMANCyc: NAMPT
Regulation	Ensembl's Regulation: ENSG00000105835
	miRBase: chr7 :105,888,731-105,925,638
	TargetScan: NM_005746
	cisRED: ENSG00000105835
Context	iHOP: NAMPT
	cancer metabolism search in PubMed: NAMPT
	UCL Cancer Institute: NAMPT
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: NAMPT
	Familial Cancer Database: NAMPT

* 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_NICOTINATE_AND_NICOTINAMIDE_METABOLISM REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS

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

Mutations for NAMPT

* 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
ovary	NAMPT	chr7	105923276	105923296	NAMPT	chr7	105923379	105923399

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 NAMPT 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
DA677790	NOP58	1	66	2	203142842	203142907	NAMPT	67	577	7	105913009	105925426
BQ335321	PLD5	250	274	1	242370111	242370136	NAMPT	263	468	7	105917540	105925393
DB135958	NAMPT	3	456	7	105913035	105925396	CD69	445	550	12	9907664	9907769
BF874906	NAMPT	25	157	7	105906073	105906205	UBE2H	150	489	7	129554703	129555042
BE940024	NAMPT	21	276	7	105907376	105907632	NAMPT	274	476	7	105907180	105907382
BQ355873	ZBTB20	280	300	3	114424119	114424139	NAMPT	282	613	7	105891622	105891952

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=32)	Stat. for Synonymous SNVs (# total SNVs=10)

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
chr7:105909679-105909679	p.L176S	3
chr7:105904020-105904020	p.E263K	2
chr7:105909680-105909680	p.L176L	2
chr7:105904030-105904030	p.K259K	2
chr7:105909656-105909656	p.D184N	1
chr7:105894856-105894856	p.L395*	1
chr7:105915391-105915391	p.?	1
chr7:105903983-105903983	p.S275Y	1
chr7:105894888-105894888	p.G384G	1
chr7:105915392-105915392	p.E106D	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=4

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		9	1		2		2			4	3	1			1	2		4
# mutation	1	1		8	1		2		2			4	3	1			1	2		4
nonsynonymous SNV	1	1		4	1		2		1			3	3	1			1	2		3
synonymous SNV				4					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
chr7:105909679	p.A286V	2
chr7:105909680	p.K259K	2
chr7:105903950	p.L176S	2
chr7:105904030	p.L176L	2
chr7:105917475	p.G355E	1
chr7:105902044	p.L131V	1
chr7:105909656	p.V95V	1
chr7:105917478	p.S275Y	1
chr7:105902057	p.E89E	1
chr7:105925305	p.E263K	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 NAMPT 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 NAMPT

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


ACSL1,AKR1B15,ATP13A4,EYS,CCDC71L,FUT3,GRAMD2, HIF1A,IDI1,LBP,MYOM2,NAMPT,PNLIPRP3,RLN3, RNASE11,RNASE12,SC5D,SRD5A1,STRA8,VLDLR,WDR91	AKIRIN1,CLDN1,COQ10B,DDX3X,ELF1,ETS2,KLF6, LDLR,MAPK1IP1L,MCL1,NAMPT,PDE12,PER2,PIGA, PNPLA8,RNF19A,SERPINB8,SGMS2,SLC25A32,TSC22D2,ZBTB21

CAPZA2,CCL20,CSF3,CXCL1,CXCL2,CXCL3,CXCL6, CCDC71L,HIF1A,IFNGR1,NAMPT,NFKBIA,NFKBIZ,PADI4, PI15,RAP1B,SOCS3,SOD2,TNFAIP1,TNFAIP3,UHRF1BP1L	ANKRD22,DNAJB11,HNRNPF,IL13RA2,LILRA5,LSM12,NAMPT, NCOA7,NMI,NUS1,PDIA6,POMP,PPA1,PSMA1, PSMA3,PSMB2,RPN1,SOD2,TIMM17A,TMED7,TSPAN8

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 NAMPT

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
DB00627	nicotinamide phosphoribosyltransferase	approved; nutraceutical; investigational	Niacin
DB00412	nicotinamide phosphoribosyltransferase	approved; investigational	Rosiglitazone

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Cross referenced IDs for NAMPT

* 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