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 AOC3
Basic gene info.Gene symbolAOC3
Gene nameamine oxidase, copper containing 3
SynonymsHPAO|SSAO|VAP-1|VAP1
CytomapUCSC genome browser: 17q21
Genomic locationchr17 :41003200-41010140
Type of geneprotein-coding
RefGenesNM_001277731.1,
NM_001277732.1,NM_003734.3,NR_102422.1,
Ensembl idENSG00000131471
Descriptionamine oxidase, copper containing 3 (vascular adhesion protein 1)copper amine oxidasemembrane primary amine oxidaseplacenta copper monamine oxidasesemicarbazide-sensitive amine oxidase
Modification date20141207
dbXrefs MIM : 603735
HGNC : HGNC
Ensembl : ENSG00000131471
HPRD : 04770
Vega : OTTHUMG00000180656
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AOC3
BioGPS: 8639
Gene Expression Atlas: ENSG00000131471
The Human Protein Atlas: ENSG00000131471
PathwayNCI Pathway Interaction Database: AOC3
KEGG: AOC3
REACTOME: AOC3
ConsensusPathDB
Pathway Commons: AOC3
MetabolismMetaCyc: AOC3
HUMANCyc: AOC3
RegulationEnsembl's Regulation: ENSG00000131471
miRBase: chr17 :41,003,200-41,010,140
TargetScan: NM_001277731
cisRED: ENSG00000131471
ContextiHOP: AOC3
cancer metabolism search in PubMed: AOC3
UCL Cancer Institute: AOC3
Assigned class in ccmGDBC

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Phenotypic Information for AOC3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AOC3
Familial Cancer Database: AOC3
* 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_TYROSINE_METABOLISM
KEGG_PHENYLALANINE_METABOLISM
KEGG_BETA_ALANINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: AOC3
MedGen: AOC3 (Human Medical Genetics with Condition)
ClinVar: AOC3
PhenotypeMGI: AOC3 (International Mouse Phenotyping Consortium)
PhenomicDB: AOC3

Mutations for AOC3
* 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 AOC3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=61)
Stat. for Synonymous SNVs
(# total SNVs=26)
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
chr17:41004204-41004204p.E282Q2
chr17:41004236-41004236p.P292P2
chr17:41004707-41004707p.S449S2
chr17:41004823-41004823p.R488Q2
chr17:41004333-41004333p.V325F2
chr17:41004722-41004722p.G454G2
chr17:41003669-41003669p.L103L2
chr17:41004468-41004468p.A370T2
chr17:41004729-41004729p.E457K2
chr17:41004340-41004340p.G327E2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample14 172 5 1  1161  178 9
# mutation14 162 5 1  1161  179 10
nonsynonymous SNV12 81 5 1  841  76 8
synonymous SNV 2 81      32   103 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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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
chr17:41004707p.A370T,AOC32
chr17:41003593p.G454G,AOC32
chr17:41004563p.R78Q,AOC32
chr17:41004722p.R258H,AOC32
chr17:41004133p.G401G,AOC32
chr17:41004468p.S449S,AOC32
chr17:41008478p.P600R,AOC31
chr17:41003847p.I6T,AOC31
chr17:41004696p.R206W,AOC31
chr17:41004165p.Y603N,AOC31

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 AOC3 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 AOC3

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

ADH1B,ADIPOQ,AOC3,AQP7,C14orf180,CIDEC,GLYAT,
GPD1,HEPACAM,ITIH5,KCNIP2,KLB,LIPE,NPR1,
PLIN1,PLIN4,RDH5,SLC19A3,TMEM132C,TNS1,VWF
ACO1,AOC3,FAM213A,DMGDH,EHD2,ESYT1,GPD1,
GYG2,HEPACAM,HEPN1,HRASLS5,LIPE,MGLL,MRAS,
PLIN1,RDH5,TNS1,TSPAN3,TUSC5,TYRO3,VKORC1L1

ACTA2,AOC3,ATP2B4,BOC,CALD1,CLIP3,CPXM2,
FERMT2,FHL1,ITGA7,KANK2,MEIS1,MSRB3,MYL9,
NEXN,PGR,RNF150,SPARCL1,TAGLN,TNS1,ZEB1
ACTN1,AOC3,ATP2B4,BVES,CACNA1C,CACNA1H,CPXM2,
DACT3,FLNA,ITGA1,ITGB3,KCNH2,LDB3,MPP2,
NPTXR,PDLIM7,PYGM,SLC8A2,TACR2,VCL,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 AOC3
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
DB00780amine oxidase, copper containing 3approvedPhenelzine
DB01275amine oxidase, copper containing 3approvedHydralazine
DB04334amine oxidase, copper containing 3experimental6-hydroxydopa quinone


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Cross referenced IDs for AOC3
* 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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