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 NMNAT1

Basic gene info.	Gene symbol	NMNAT1
	Gene name	nicotinamide nucleotide adenylyltransferase 1
	Synonyms	LCA9\|NMNAT\|PNAT1
	Cytomap	UCSC genome browser: 1p36.22
	Genomic location	chr1 :10003485-10045556
	Type of gene	protein-coding
	RefGenes	NM_001297778.1, NM_001297779.1,NM_022787.3,
	Ensembl id	ENSG00000173614
	Description	NMN adenylyltransferase 1NaMN adenylyltransferase 1nicotinamide mononucleotide adenylyltransferase 1nicotinate-nucleotide adenylyltransferase 1pyridine nucleotide adenylyltransferase 1
	Modification date	20141207
dbXrefs	MIM : 608700
	HGNC : HGNC
	Ensembl : ENSG00000173614
	HPRD : 16369
	Vega : OTTHUMG00000001799
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NMNAT1
	BioGPS: 64802
	Gene Expression Atlas: ENSG00000173614
	The Human Protein Atlas: ENSG00000173614
Pathway	NCI Pathway Interaction Database: NMNAT1
	KEGG: NMNAT1
	REACTOME: NMNAT1
	ConsensusPathDB
	Pathway Commons: NMNAT1
Metabolism	MetaCyc: NMNAT1
	HUMANCyc: NMNAT1
Regulation	Ensembl's Regulation: ENSG00000173614
	miRBase: chr1 :10,003,485-10,045,556
	TargetScan: NM_001297778
	cisRED: ENSG00000173614
Context	iHOP: NMNAT1
	cancer metabolism search in PubMed: NMNAT1
	UCL Cancer Institute: NMNAT1
Assigned class in ccmGDB	C

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Phenotypic Information for NMNAT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: NMNAT1
	Familial Cancer Database: NMNAT1

* 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: NMNAT1
	MedGen: NMNAT1 (Human Medical Genetics with Condition)
	ClinVar: NMNAT1
Phenotype	MGI: NMNAT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: NMNAT1

Mutations for NMNAT1

* 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 NMNAT1 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
BJ997860	SMA4	1	300	5	70220889	70237320	NMNAT1	295	600	1	10044392	10044697
BQ372419	TPM1	10	290	15	63348595	63349095	NMNAT1	272	301	1	10009046	10009075

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

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

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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=15)	Stat. for Synonymous SNVs (# total SNVs=4)

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
chr1:10042579-10042579	p.D220E	2
chr1:10042513-10042513	p.Y198*	1
chr1:10035791-10035791	p.E86A	1
chr1:10042553-10042553	p.V212M	1
chr1:10035808-10035808	p.W92R	1
chr1:10035810-10035810	p.W92C	1
chr1:10042629-10042629	p.R237H	1
chr1:10041188-10041188	p.Q133Q	1
chr1:10042655-10042655	p.E246*	1
chr1:10041198-10041198	p.Q137E	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		1	1	2			3					4					1	2		5
# mutation		1	1	2			3					4					1	2		5
nonsynonymous SNV		1		2			3					3						1		3
synonymous SNV			1									1					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
chr1:10042490	p.E86A	1
chr1:10035759	p.E91D	1
chr1:10042553	p.W92R	1
chr1:10035791	p.W92C	1
chr1:10042584	p.Q133Q	1
chr1:10035807	p.K138N	1
chr1:10042669	p.S162F	1
chr1:10035808	p.I177I	1
chr1:10042714	p.G182E	1
chr1:10035810	p.N191D	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 NMNAT1 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 NMNAT1

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


DNAJC16,EXOSC10,FBXO42,GNB1,HMGCL,ICMT,CEP104, LZIC,MED18,MFN2,MTHFR,MTOR,NMNAT1,PHACTR4, PRDM2,RERE,SLC35E2,UBE4B,USP48,VPS13D,ZBTB40	ALDH5A1,CUL4A,FECH,HBS1L,KLHL31,LOC729082,LYRM7, NDUFS1,NMNAT1,NNT,PCBD2,PDHX,PRKAB2,PRKAR2A, PTCD3,RHOBTB1,SGCD,UBR3,USO1,ZNF106,ZYG11B

ABCD3,ATP5F1,MPC1,MINOS1,CDC42,DNAJC11,DNAJC16, ETFDH,FUCA1,HADH,HMGCL,LZIC,MED18,NMNAT1, OMA1,PAFAH2,PGD,PXMP2,SDHB,SLC35A3,TMEM106C	AIMP2,ALG14,BPNT1,MPC1,TMEM251,C15orf48,ABRACL, MICU2,ETFA,FAM195A,LGALS3,MGST3,MLX,NMNAT1, NRAS,SLC25A16,SLMO2,SRI,UOX,UQCRC2,UQCRFS1

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 NMNAT1

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 1	experimental	Nicotinamide-Adenine-Dinucleotide
DB03227	nicotinamide nucleotide adenylyltransferase 1	experimental	Nicotinamide Mononucleotide
DB04099	nicotinamide nucleotide adenylyltransferase 1	experimental	Deamido-Nad+
DB00160	nicotinamide nucleotide adenylyltransferase 1	approved; nutraceutical	L-Alanine
DB00130	nicotinamide nucleotide adenylyltransferase 1	approved; nutraceutical; investigational	L-Glutamine
DB00150	nicotinamide nucleotide adenylyltransferase 1	approved; nutraceutical	L-Tryptophan

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Cross referenced IDs for NMNAT1

* 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