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 NMNAT2

Basic gene info.	Gene symbol	NMNAT2
	Gene name	nicotinamide nucleotide adenylyltransferase 2
	Synonyms	C1orf15\|PNAT2
	Cytomap	UCSC genome browser: 1q25
	Genomic location	chr1 :183217371-183387634
	Type of gene	protein-coding
	RefGenes	NM_015039.3, NM_170706.3,
	Ensembl id	ENSG00000157064
	Description	NMN adenylyltransferase 2NaMN adenylyltransferase 2nicotinamide mononucleotide adenylyltransferase 2nicotinate-nucleotide adenylyltransferase 2pyridine nucleotide adenylyltransferase 2
	Modification date	20141207
dbXrefs	MIM : 608701
	HGNC : HGNC
	Ensembl : ENSG00000157064
	HPRD : 09786
	Vega : OTTHUMG00000035519
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NMNAT2
	BioGPS: 23057
	Gene Expression Atlas: ENSG00000157064
	The Human Protein Atlas: ENSG00000157064
Pathway	NCI Pathway Interaction Database: NMNAT2
	KEGG: NMNAT2
	REACTOME: NMNAT2
	ConsensusPathDB
	Pathway Commons: NMNAT2
Metabolism	MetaCyc: NMNAT2
	HUMANCyc: NMNAT2
Regulation	Ensembl's Regulation: ENSG00000157064
	miRBase: chr1 :183,217,371-183,387,634
	TargetScan: NM_015039
	cisRED: ENSG00000157064
Context	iHOP: NMNAT2
	cancer metabolism search in PubMed: NMNAT2
	UCL Cancer Institute: NMNAT2
Assigned class in ccmGDB	C

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Phenotypic Information for NMNAT2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: NMNAT2
	Familial Cancer Database: NMNAT2

* 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: NMNAT2
	MedGen: NMNAT2 (Human Medical Genetics with Condition)
	ClinVar: NMNAT2
Phenotype	MGI: NMNAT2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: NMNAT2

Mutations for NMNAT2

* 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	NMNAT2	chr1	183230950	183230970		chr1	182930055	182930075
ovary	NMNAT2	chr1	183245960	183245980	NMNAT2	chr1	183246012	183246032
ovary	NMNAT2	chr1	183330104	183330124		chr18	11213	11233
ovary	NMNAT2	chr1	183330253	183330273		chr20	57220837	57220857
ovary	NMNAT2	chr1	183378265	183378285		chr1	182730278	182730298

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 NMNAT2 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
CN288204	FUS	2	440	16	31191468	31195568	NMNAT2	434	538	1	183218278	183218381
AK126960	UNC13C	1	2048	15	54386087	54388134	NMNAT2	2041	2737	1	183217373	183218069

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=37)	Stat. for Synonymous SNVs (# total SNVs=15)

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
chr1:183221856-183221856	p.G282S	4
chr1:183253160-183253160	p.L182M	3
chr1:183262858-183262858	p.H52H	3
chr1:183253165-183253165	p.A180V	2
chr1:183221827-183221827	p.P291P	2
chr1:183230397-183230397	p.P231P	2
chr1:183259275-183259275	p.R103R	2
chr1:183253905-183253905	p.G157R	2
chr1:183387360-183387360	p.G15C	2
chr1:183230196-183230196	p.I254M	2

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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		1		6	1		1		1		1	8	2	1			4	2		6
# mutation		1		6	1		1		1		1	8	3	1			4	2		5
nonsynonymous SNV		1		5					1		1	6	2	1			3	2		3
synonymous SNV				1	1		1					2	1				1			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
chr1:183255900	p.S115S,NMNAT2	2
chr1:183253165	p.G282S,NMNAT2	2
chr1:183221856	p.H52H,NMNAT2	2
chr1:183262858	p.A180V,NMNAT2	2
chr1:183230190	p.V156V,NMNAT2	1
chr1:183253890	p.T4T	1
chr1:183262892	p.S115Y,NMNAT2	1
chr1:183230359	p.N262H,NMNAT2	1
chr1:183253906	p.S97R,NMNAT2	1
chr1:183387338	p.V256V,NMNAT2	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 NMNAT2 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 NMNAT2

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


AP3B2,APLP1,BSN,CHRNB2,DDX25,AMER3,GNAO1, UNC79,NMNAT2,PCDH9,RAB34___RAB39A,RIPPLY2,RUNDC3A,SCG3, SCN3B,SNAP25,SYN1,SYP,SYT4,TMEM145,UNC13A	ANO6,ARHGAP31,BTNL9,PQLC2L,CAT,CD300LG,CRYBG3, EBF1,FERMT2,GJC1,HSD17B13,KCNIP2,KIAA1462,NMNAT2, PDE3B,PDE8A,PPP2R5A,SH3KBP1,SIK2,STXBP1,TYRO3

BSN,CAMKV,ERC2,AMER3,GRM4,KCNC1,KCNH6, LOC254559,NMNAT2,PRMT8,RAB3C,RPRML,SCG3,SCN3B, SLC6A15,SNAP25,SVOP,SYP,SLC35G2,VGF,XKR7	ANK2,ARHGAP6,C20orf194,CDON,FAM129A,FAM131B,HDAC4, ITPKB,MTCL1,LONRF2,MASP1,MYOCD,NMNAT2,NRXN1, PRDM6,PTCHD1,SSC5D,WBSCR17,WHAMMP3,ZBTB47,ZMAT4

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 NMNAT2

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
DB00160	nicotinamide nucleotide adenylyltransferase 2	approved; nutraceutical	L-Alanine
DB00130	nicotinamide nucleotide adenylyltransferase 2	approved; nutraceutical; investigational	L-Glutamine
DB00150	nicotinamide nucleotide adenylyltransferase 2	approved; nutraceutical	L-Tryptophan

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Cross referenced IDs for NMNAT2

* 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