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 NMNAT3

Basic gene info.	Gene symbol	NMNAT3
	Gene name	nicotinamide nucleotide adenylyltransferase 3
	Synonyms	PNAT-3\|PNAT3
	Cytomap	UCSC genome browser: 3q23
	Genomic location	chr3 :139279022-139396885
	Type of gene	protein-coding
	RefGenes	NM_001200047.1, NM_178177.3,
	Ensembl id	ENSG00000163864
	Description	NMN adenylyltransferase 3NaMN adenylyltransferase 3nicotinamide mononucleotide adenylyltransferase 3nicotinate-nucleotide adenylyltransferase 3pyridine nucleotide adenylyltransferase 3
	Modification date	20141207
dbXrefs	MIM : 608702
	HGNC : HGNC
	Ensembl : ENSG00000163864
	HPRD : 16370
	Vega : OTTHUMG00000159951
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NMNAT3
	BioGPS: 349565
	Gene Expression Atlas: ENSG00000163864
	The Human Protein Atlas: ENSG00000163864
Pathway	NCI Pathway Interaction Database: NMNAT3
	KEGG: NMNAT3
	REACTOME: NMNAT3
	ConsensusPathDB
	Pathway Commons: NMNAT3
Metabolism	MetaCyc: NMNAT3
	HUMANCyc: NMNAT3
Regulation	Ensembl's Regulation: ENSG00000163864
	miRBase: chr3 :139,279,022-139,396,885
	TargetScan: NM_001200047
	cisRED: ENSG00000163864
Context	iHOP: NMNAT3
	cancer metabolism search in PubMed: NMNAT3
	UCL Cancer Institute: NMNAT3
Assigned class in ccmGDB	C

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Phenotypic Information for NMNAT3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: NMNAT3
	Familial Cancer Database: NMNAT3

* 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: NMNAT3
	MedGen: NMNAT3 (Human Medical Genetics with Condition)
	ClinVar: NMNAT3
Phenotype	MGI: NMNAT3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: NMNAT3

Mutations for NMNAT3

* 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	NMNAT3	chr3	139336883	139336883	NMNAT3	chr3	139341805	139341805
ovary	NMNAT3	chr3	139322055	139322075	CDH12	chr5	22809239	22809259
ovary	NMNAT3	chr3	139332939	139332959		chr8	33564678	33564698
pancreas	NMNAT3	chr3	139302618	139302638	NMNAT3	chr3	139302328	139302348
pancreas	NMNAT3	chr3	139352683	139352703	NMNAT3	chr3	139354170	139354190

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 NMNAT3 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
BF576138	CCDC36	2	50	3	49236958	49237006	NMNAT3	49	619	3	139279664	139280236
BM544763	MAG	16	136	19	35785138	35786353	NMNAT3	137	877	3	139279838	139396595

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=12)	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
chr3:139297857-139297857	p.N13N	3
chr3:139297737-139297737	p.W53*	3
chr3:139297773-139297773	p.I41I	2
chr3:139279867-139279867	p.E211D	2
chr3:139297817-139297817	p.R27*	2
chr3:139279992-139279992	p.R170*	1
chr3:139297755-139297755	p.E47E	1
chr3:139297856-139297856	p.D14N	1
chr3:139280106-139280106	p.G132C	1
chr3:139297758-139297758	p.W46*	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=2

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				2	1				1			2	2				11	2
# mutation				2	1				1			2	2				13	2
nonsynonymous SNV				2					1			1	1				6	1
synonymous SNV					1							1	1				7	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
chr3:139297773	p.I41I	2
chr3:139280028	p.Q73Q	1
chr3:139297857	p.A51V	1
chr3:139280118	p.Q50Q	1
chr3:139297865	p.P45P	1
chr3:139280150	p.Q36H	1
chr3:139297868	p.G17G	1
chr3:139292486	p.E159D,NMNAT3	1
chr3:139297869	p.D14N	1
chr3:139297744	p.T149N,NMNAT3	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 NMNAT3 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 NMNAT3

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


ASB13,BCL2,CLSTN2,DBNDD2,DCAKD,DNALI1,FAM110B, FUZ,GATA3,KDM4B,LOC100190938,LOC284440,LYPD6,LYPD6B, MYB,MYOZ3,NMNAT3,STK32B,TLE3,TMEM26,TRIM45	AKAP1,ANAPC16,CNBP,FAF1,FBXO42,HADHA,LIAS, MCEE,NDUFS4,NMNAT3,OXA1L,POLR2C,SAMM50,SCMH1, SLC25A23,SLC25A26,SLC25A42,SRP68,TARSL2,UQCRC2,VDAC2

ASPSCR1,AXIN2,BAMBI,CAB39L,DACH1,DDX31,KRT32, KRT35,LINC01512,MSX2,MSX2P1,NCKAP5,NMNAT3,KIZ, RPL12,SESN1,SNTB1,SP5,SYK,TCEAL1,TCF7	AGBL5,FAM210B,DHX40,DVL2,GAL3ST4,GNPAT,LOC284023, LOC400027,MBTPS1,EPB41L4A-AS1,NMNAT3,POLL,PPOX,SLC41A3, SNAP47,TAB1,TRAK2,YPEL1,ZDHHC1,ZNF345,ZNF559

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 NMNAT3

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
DB01907	nicotinamide nucleotide adenylyltransferase 3	experimental	Nicotinamide-Adenine-Dinucleotide
DB02596	nicotinamide nucleotide adenylyltransferase 3	experimental	Alpha,Beta-Methyleneadenosine-5'-Triphosphate
DB03227	nicotinamide nucleotide adenylyltransferase 3	experimental	Nicotinamide Mononucleotide
DB04099	nicotinamide nucleotide adenylyltransferase 3	experimental	Deamido-Nad+
DB00160	nicotinamide nucleotide adenylyltransferase 3	approved; nutraceutical	L-Alanine
DB00130	nicotinamide nucleotide adenylyltransferase 3	approved; nutraceutical; investigational	L-Glutamine
DB00150	nicotinamide nucleotide adenylyltransferase 3	approved; nutraceutical	L-Tryptophan

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Cross referenced IDs for NMNAT3

* 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