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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
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 | Significant driver gene in |
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) |
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 |
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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 |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=15) | (# total SNVs=4) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr1:10041203-10041203 | p.K138N | 1 |
chr1:10042669-10042669 | p.K250N | 1 |
chr1:10042450-10042450 | p.I177I | 1 |
chr1:10042683-10042683 | p.S255N | 1 |
chr1:10032143-10032143 | p.S4S | 1 |
chr1:10042464-10042464 | p.G182E | 1 |
chr1:10042714-10042714 | p.V265V | 1 |
chr1:10032227-10032227 | p.K32K | 1 |
chr1:10042475-10042475 | p.V186I | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |
chr1:10041188 | p.S162F | 1 |
chr1:10041203 | p.I177I | 1 |
chr1:10032143 | p.G182E | 1 |
chr1:10042404 | p.N191D | 1 |
chr1:10032227 | p.V212M | 1 |
chr1:10042450 | p.S4S | 1 |
chr1:10032236 | p.S222L | 1 |
chr1:10042464 | p.K32K | 1 |
chr1:10035738 | p.K250N | 1 |
chr1:10042490 | p.M35I | 1 |
Other DBs for Point Mutations |
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. |
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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 |
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 |
* 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 |
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Interacting Genes (from Pathway Commons) |
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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 |
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