Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 NOS1
Basic gene info.Gene symbolNOS1
Gene namenitric oxide synthase 1 (neuronal)
SynonymsIHPS1|N-NOS|NC-NOS|NOS|bNOS|nNOS
CytomapUCSC genome browser: 12q24.22
Genomic locationchr12 :117645946-117799607
Type of geneprotein-coding
RefGenesNM_000620.4,
NM_001204213.1,NM_001204214.1,NM_001204218.1,
Ensembl idENSG00000089250
DescriptionNOS type Iconstitutive NOSneuronal NOSnitric oxide synthase, brainpeptidyl-cysteine S-nitrosylase NOS1
Modification date20141207
dbXrefs MIM : 163731
HGNC : HGNC
Ensembl : ENSG00000089250
HPRD : 01226
Vega : OTTHUMG00000137376
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NOS1
BioGPS: 4842
Gene Expression Atlas: ENSG00000089250
The Human Protein Atlas: ENSG00000089250
PathwayNCI Pathway Interaction Database: NOS1
KEGG: NOS1
REACTOME: NOS1
ConsensusPathDB
Pathway Commons: NOS1
MetabolismMetaCyc: NOS1
HUMANCyc: NOS1
RegulationEnsembl's Regulation: ENSG00000089250
miRBase: chr12 :117,645,946-117,799,607
TargetScan: NM_000620
cisRED: ENSG00000089250
ContextiHOP: NOS1
cancer metabolism search in PubMed: NOS1
UCL Cancer Institute: NOS1
Assigned class in ccmGDBC

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Phenotypic Information for NOS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NOS1
Familial Cancer Database: NOS1
* 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/

check002.gifMetabolic Pathway Description
KEGG_ARGININE_AND_PROLINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NOS1
MedGen: NOS1 (Human Medical Genetics with Condition)
ClinVar: NOS1
PhenotypeMGI: NOS1 (International Mouse Phenotyping Consortium)
PhenomicDB: NOS1

Mutations for NOS1
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryNOS1chr12117750588117750608NOS1chr12117747788117747808
ovaryNOS1chr12117750780117750800chr12117803536117803556
pancreasNOS1chr12117728864117728884NOS1chr12117729498117729518
pancreasNOS1chr12117754994117755014NOS1chr12117755571117755591
pancreasNOS1chr12117789990117790010chr12128128128128128148
pancreasNOS1chr12117790467117790487chr129084564790845667
pancreasNOS1chr12117790500117790520NOS1chr12117790951117790971
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NOS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF930971NOS11419812117649316117649500NFE2L1192444174613473146135775

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1     1  
GAIN (# sample)        1     1  
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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check002.gifSNV 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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=202)
Stat. for Synonymous SNVs
(# total SNVs=78)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr12:117696917-117696917p.Y796H8
chr12:117698325-117698325p.S771L6
chr12:117710315-117710315p.V572M6
chr12:117768733-117768733p.R48C5
chr12:117723955-117723955p.R415Q4
chr12:117672461-117672461p.L1048L4
chr12:117681140-117681140p.R975H3
chr12:117685236-117685236p.E914K3
chr12:117724063-117724063p.S379F3
chr12:117672544-117672544p.R1021C3

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample57 259 2 1221271332 6023221
# mutation57 339 2 1221261332 9027226
nonsynonymous SNV46 215 2 91116921 5217115
synonymous SNV11 124   31 10411 3810111
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr12:117723955p.E578K,NOS13
chr12:117710315p.R79Q,NOS13
chr12:117685236p.V236M,NOS13
chr12:117655926p.R1069Q,NOS13
chr12:117718572p.E328K,NOS12
chr12:117723943p.E496K,NOS12
chr12:117703242p.P125P,NOS12
chr12:117672562p.V264I,NOS12
chr12:117710231p.S82S,NOS12
chr12:117723945p.F305L,NOS12

check002.gifOther 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

check002.gifCopy Number for NOS1 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 NOS1

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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

ADCY3,CD14,CD180,DMBT1,EDN3,GNLY,IGFL4,
KIR2DL3,LIPG,MRGPRX3,NOS1,OLAH,PDE11A,PGA5,
PTN,SST,TGFBR2,TMEM100,TMEM233,VNN1,XDH
ABRA,ANKRD23,ASB15,MLIP,CAV3,CHRNG,DUSP26,
FBXO40,HSPB3,ITGB1BP2,NMRK2,KLHL34,KLHL38,LDB3,
MYOZ1,NOS1,NT5C1A,RAPSN,SRL,TMEM38A,TRIM54

CCNA1,CHRNA3,CNTNAP5,DPP6,GAP43,GNG3,KIF5A,
NEFM,NGB,NOS1,PENK,PHOX2A,PHOX2B,PRPH,
SLC18A3,SLC5A7,SLITRK3,SOX10,ST8SIA3,STMN4,SYT9
ABCC9,ACTA2,AOC3,SKIDA1,C20orf166-AS1,CNTNAP1,CNTNAP5,
FBXL22,GPR156,RBFOX3,ITGB3,LOC100192378,LOXL4,NLGN1,
NOS1,SCUBE3,TAGLN,TMEM200B,TMTC2,TRPC4,ZFHX4
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting 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 NOS1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00155nitric oxide synthase 1 (neuronal)approved; nutraceuticalL-Citrulline
DB01821nitric oxide synthase 1 (neuronal)experimentalL-N(Omega)-Nitroarginine-2,4-L-Diaminobutyric Amide
DB01942nitric oxide synthase 1 (neuronal)experimentalFormic Acid
DB01997nitric oxide synthase 1 (neuronal)experimental3-Bromo-7-Nitroindazole
DB02027nitric oxide synthase 1 (neuronal)experimentalN-{(4s)-4-Amino-5-[(2-Aminoethyl)Amino]Pentyl}-N'-Nitroguanidine
DB02044nitric oxide synthase 1 (neuronal)experimentalN-(3-(Aminomethyl)Benzyl)Acetamidine
DB02077nitric oxide synthase 1 (neuronal)experimentalL-N(Omega)-Nitroarginine-(4r)-Amino-L-Proline Amide
DB02143nitric oxide synthase 1 (neuronal)experimentalN-Isopropyl-N'-Hydroxyguanidine
DB02644nitric oxide synthase 1 (neuronal)experimentalN-Omega-Propyl-L-Arginine
DB02692nitric oxide synthase 1 (neuronal)experimental(6r,1'r,2's)-5,6,7,8 Tetrahydrobiopterin
DB02727nitric oxide synthase 1 (neuronal)experimentalN-Butyl-N'-Hydroxyguanidine
DB02944nitric oxide synthase 1 (neuronal)experimentalAlpha-D-Mannose
DB02991nitric oxide synthase 1 (neuronal)experimentalS-Ethyl-N-[4-(Trifluoromethyl)Phenyl]Isothiourea
DB03014nitric oxide synthase 1 (neuronal)experimentalHeme
DB03144nitric oxide synthase 1 (neuronal)experimentalN-Omega-Hydroxy-L-Arginine
DB03147nitric oxide synthase 1 (neuronal)experimentalFlavin-Adenine Dinucleotide
DB03247nitric oxide synthase 1 (neuronal)experimentalRiboflavin Monophosphate
DB03449nitric oxide synthase 1 (neuronal)experimentalN-(4-(2-((3-Chlorophenylmethyl)Amino)Ethyl)Phenyl)-2-Thiophecarboxamidine
DB03461nitric oxide synthase 1 (neuronal)experimental2'-Monophosphoadenosine 5'-Diphosphoribose
DB03707nitric oxide synthase 1 (neuronal)experimentalS-Ethyl-N-Phenyl-Isothiourea
DB03710nitric oxide synthase 1 (neuronal)experimentalN5-(1-Imino-3-Butenyl)-L-Ornithine
DB03892nitric oxide synthase 1 (neuronal)experimental5-N-Allyl-Arginine
DB04223nitric oxide synthase 1 (neuronal)experimentalNitroarginine
DB08018nitric oxide synthase 1 (neuronal)experimentalN-{(3S,4S)-4-[(6-AMINO-4-METHYLPYRIDIN-2-YL)METHYL]PYRROLIDIN-3-YL}-N'-(4-CHLOROBENZYL)ETHANE-1,2-DIAMINE
DB08019nitric oxide synthase 1 (neuronal)experimentalN-{(3R,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-(3-chlorobenzyl)ethane-1,2-diamine
DB00997nitric oxide synthase 1 (neuronal)approved; investigationalDoxorubicin
DB00171nitric oxide synthase 1 (neuronal)approved; nutraceuticalAdenosine triphosphate
DB00125nitric oxide synthase 1 (neuronal)approved; nutraceuticalL-Arginine
DB00435nitric oxide synthase 1 (neuronal)approvedNitric Oxide


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Cross referenced IDs for NOS1
* 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



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