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 AOX1
Basic gene info.Gene symbolAOX1
Gene namealdehyde oxidase 1
SynonymsAO|AOH1
CytomapUCSC genome browser: 2q33
Genomic locationchr2 :201450730-201536217
Type of geneprotein-coding
RefGenesNM_001159.3,
Ensembl idENSG00000138356
Descriptionaldehyde oxidaseazaheterocycle hydroxylase
Modification date20141207
dbXrefs MIM : 602841
HGNC : HGNC
Ensembl : ENSG00000138356
HPRD : 07537
Vega : OTTHUMG00000154536
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AOX1
BioGPS: 316
Gene Expression Atlas: ENSG00000138356
The Human Protein Atlas: ENSG00000138356
PathwayNCI Pathway Interaction Database: AOX1
KEGG: AOX1
REACTOME: AOX1
ConsensusPathDB
Pathway Commons: AOX1
MetabolismMetaCyc: AOX1
HUMANCyc: AOX1
RegulationEnsembl's Regulation: ENSG00000138356
miRBase: chr2 :201,450,730-201,536,217
TargetScan: NM_001159
cisRED: ENSG00000138356
ContextiHOP: AOX1
cancer metabolism search in PubMed: AOX1
UCL Cancer Institute: AOX1
Assigned class in ccmGDBC

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Phenotypic Information for AOX1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AOX1
Familial Cancer Database: AOX1
* 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_TYROSINE_METABOLISM
KEGG_TRYPTOPHAN_METABOLISM
KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM
KEGG_DRUG_METABOLISM_CYTOCHROME_P450

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: AOX1
MedGen: AOX1 (Human Medical Genetics with Condition)
ClinVar: AOX1
PhenotypeMGI: AOX1 (International Mouse Phenotyping Consortium)
PhenomicDB: AOX1

Mutations for AOX1
* 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
* 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryAOX1chr2201475999201476019AOX1chr2201473448201473468
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 AOX1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AV653907AOX113642201534428201535676ALB36270647428394474286870

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 # sample1       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=131)
Stat. for Synonymous SNVs
(# total SNVs=29)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

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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
chr2:201478598-201478598p.A507V5
chr2:201478599-201478599p.A507A3
chr2:201485877-201485877p.G637S3
chr2:201524742-201524742p.R1109C3
chr2:201460056-201460056p.M55I3
chr2:201460064-201460064p.R58Q3
chr2:201505907-201505907p.F885F2
chr2:201464445-201464445p.D138N2
chr2:201507524-201507524p.K949N2
chr2:201477456-201477456p.Y463C2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample441165 6 71 2014511298214
# mutation541174 7 71 20155113112222
nonsynonymous SNV33 113 5 7  1214511207117
synonymous SNV21161 2  1 81   11515
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
chr2:201485877p.K949E2
chr2:201457926p.K949N2
chr2:201460056p.Y463C2
chr2:201478598p.S287Y2
chr2:201470304p.A507V2
chr2:201507522p.G637C2
chr2:201468754p.L35F2
chr2:201507524p.M55I2
chr2:201477456p.L201L2
chr2:201507454p.E1111K1

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 AOX1 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 AOX1

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

AOX1,ASB9,C17orf98,CEACAM3,CNIH1,CWC25,DNAJC22,
FKBP1A,GK,GK3P,KIR3DL2,LIG3,LOC728276,MRPL45,
RAD51D,RFFL,SLC13A2,SLC25A18,SLC34A2,TMC2,ZNF830
ABCA6,ABCA8,AOX1,CCDC80,CRTAP,CYBRD1,DSE,
DUSP22,EMX2OS,FBLN5,GALNT15,NEGR1,NOX4,PCSK5,
PID1,PRELP,SLC9A9,SNX9,TGFBR2,TIMP2,XG

ABCA6,ABCA8,ABCA9,ADH1B,AOX1,MEDAG,C7,
CCDC80,CDO1,EFEMP1,FBLN5,FZD4,IGF1,LHFP,
LOC339524,PALMD,PODN,RBMS3,SFRP1,SLIT3,SVEP1
ADAMTS5,AEBP1,AOX1,BGN,C1R,C3,CYP1B1,
EBF1,EDNRA,EFEMP1,FAM198A,GPR116,GPX3,IL1R1,
LAMA2,LRRC32,PDGFRB,SERPINF1,SRL,STEAP4,THSD7A
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 AOX1
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
DB00993aldehyde oxidase 1approvedAzathioprine
DB00437aldehyde oxidase 1approvedAllopurinol
DB00170aldehyde oxidase 1approved; nutraceuticalMenadione
DB00563aldehyde oxidase 1approvedMethotrexate
DB00352aldehyde oxidase 1approvedThioguanine


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Cross referenced IDs for AOX1
* 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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