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 DAO
Basic gene info.Gene symbolDAO
Gene nameD-amino-acid oxidase
SynonymsDAAO|DAMOX|OXDA
CytomapUCSC genome browser: 12q24
Genomic locationchr12 :109273856-109294710
Type of geneprotein-coding
RefGenesNM_001917.4,
Ensembl idENSG00000110887
DescriptionD-amino acid oxidase
Modification date20141207
dbXrefs MIM : 124050
HGNC : HGNC
Ensembl : ENSG00000110887
HPRD : 15917
Vega : OTTHUMG00000169360
ProteinUniProt: P14920
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DAO
BioGPS: 1610
Gene Expression Atlas: ENSG00000110887
The Human Protein Atlas: ENSG00000110887
PathwayNCI Pathway Interaction Database: DAO
KEGG: DAO
REACTOME: DAO
ConsensusPathDB
Pathway Commons: DAO
MetabolismMetaCyc: DAO
HUMANCyc: DAO
RegulationEnsembl's Regulation: ENSG00000110887
miRBase: chr12 :109,273,856-109,294,710
TargetScan: NM_001917
cisRED: ENSG00000110887
ContextiHOP: DAO
cancer metabolism search in PubMed: DAO
UCL Cancer Institute: DAO
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DAO in cancer cell metabolism1. Fang J, Nakamura H, Iyer AK (2007) Tumor-targeted induction of oxystress for cancer therapy. J Drug Target 15: 475-486. doi: 10.1080/10611860701498286. go to article
2. El Sayed SM, El-Magd RM, Shishido Y, Chung SP, Diem TH, et al. (2012) 3-Bromopyruvate antagonizes effects of lactate and pyruvate, synergizes with citrate and exerts novel anti-glioma effects. J Bioenerg Biomembr 44: 61-79. doi: 10.1007/s10863-012-9409-4. go to article
3. El Sayed SM, El-Magd RM, Shishido Y, Yorita K, Chung SP, et al. (2012) D-Amino acid oxidase-induced oxidative stress, 3-bromopyruvate and citrate inhibit angiogenesis, exhibiting potent anticancer effects. J Bioenerg Biomembr 44: 513-523. doi: 10.1007/s10863-012-9455-y. go to article
4. El Sayed SM, Abou El-Magd RM, Shishido Y, Chung SP, Sakai T, et al. (2012) D-amino acid oxidase gene therapy sensitizes glioma cells to the antiglycolytic effect of 3-bromopyruvate. Cancer Gene Ther 19: 1-18. doi: 10.1038/cgt.2011.59. go to article
5. Fang J, Seki T, Maeda H (2009) Therapeutic strategies by modulating oxygen stress in cancer and inflammation. Adv Drug Deliv Rev 61: 290-302. doi: 10.1016/j.addr.2009.02.005. go to article

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Phenotypic Information for DAO(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DAO
Familial Cancer Database: DAO
* 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_GLYCINE_SERINE_AND_THREONINE_METABOLISM
KEGG_ARGININE_AND_PROLINE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM 124050; gene.
Orphanet 803; Amyotrophic lateral sclerosis.
DiseaseKEGG Disease: DAO
MedGen: DAO (Human Medical Genetics with Condition)
ClinVar: DAO
PhenotypeMGI: DAO (International Mouse Phenotyping Consortium)
PhenomicDB: DAO

Mutations for DAO
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DAO related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
X13227MT1G181165670189556701975DAO76162912109273885109294697
AX786389MT1G181165670189556701975DAO76162912109273885109294697

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

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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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=52)
Stat. for Synonymous SNVs
(# total SNVs=14)
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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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
chr12:109293186-109293186p.R283W3
chr12:109293196-109293196p.R286H3
chr12:109288048-109288048p.E173K3
chr12:109283320-109283320p.G129C3
chr12:109278816-109278816p.G12R3
chr12:109288126-109288126p.R199W2
chr12:109292540-109292540p.E261K2
chr12:109293195-109293195p.R286C2
chr12:109283296-109283296p.E121*2
chr12:109293207-109293207p.R290W2

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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
# sample 2154 1 1  511 296 8
# mutation 2164 1 1  611 2116 10
nonsynonymous SNV  164   1  31  196 9
synonymous SNV 2    1    3 1 12  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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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
chr12:109293196p.R286H2
chr12:109293207p.R290W2
chr12:109293228p.R297C2
chr12:109286790p.R162Q2
chr12:109288048p.E173K2
chr12:109294262p.A36T1
chr12:109283259p.A188A1
chr12:109290788p.T45T1
chr12:109278864p.R199W1
chr12:109293195p.D46N1

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 DAO 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 DAO

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

AHSG,APOA1,APOA2,APOC3,APOC4,ASGR2,DAO,
F2,HAMP,HRG,ITIH1,ITIH3,KNG1,LEAP2,
PLG,SERPINC1,SLC17A2,SLC22A7,SLC2A2,SPP2,SULT2A1
ADRA1D,BEX1,PRR35,CACNA1H,CHRNA9,COL2A1,CST9,
DAO,DEFB4A,FAM135B,FCRLB,GLDC,HBQ1,LRTM2,
SLC6A4,SLIT1,SPDYC,TCL1B,TTLL8,WFDC11,ZNF479

AQP8,C1orf106,CDHR5,CTXN2,DAO,DIO3OS,DIRAS2,
ENAM,FAM132A,G6PC,KCTD4,LPGAT1,LRRN2,PCDHA10,
PCDHGB4,PHLPP2,PTPN14,SCARNA21,SLC16A4,SOX3,TBPL2
ANXA11,ATP6V0D1,CA4,CLIC5,CORO1B,DAO,IFI27,
LRRC56,MYD88,OAS1,PLAC8,PPP1R14D,RAB4B,RALY,
SH3BP1,TDRD7,TEX11,TJP3,TMEM54,TRIM31,TWF2
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 DAO
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P14920; -.
ChemistryChEMBL CHEMBL5485; -.
Organism-specific databasesPharmGKB PA27139; -.
Organism-specific databasesCTD 1610; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02838D-amino-acid oxidaseexperimental3,4-Dihydro-2h-Pyrrolium-5-Carboxylate
DB02988D-amino-acid oxidaseexperimentalImino-Tryptophan
DB03147D-amino-acid oxidaseexperimentalFlavin-Adenine Dinucleotide
DB03225D-amino-acid oxidaseexperimentalD-Tryptophan
DB03531D-amino-acid oxidaseexperimentalFlavin-Adenine Dinucleotide-N5-Isobutyl Ketone
DB03793D-amino-acid oxidaseexperimentalBenzoic Acid
DB04166D-amino-acid oxidaseexperimental2-Aminobenzoic Acid
DB07979D-amino-acid oxidaseexperimental(2E)-3-(3,4-DIHYDROXYPHENYL)-2-IMINOPROPANOIC ACID
DB00145D-amino-acid oxidaseapproved; nutraceuticalGlycine
DB00160D-amino-acid oxidaseapproved; nutraceuticalL-Alanine


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Cross referenced IDs for DAO
* 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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