Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 ACOX3
Basic gene info.Gene symbolACOX3
Gene nameacyl-CoA oxidase 3, pristanoyl
Synonyms-
CytomapUCSC genome browser: 4p15.3
Genomic locationchr4 :8368008-8442452
Type of geneprotein-coding
RefGenesNM_001101667.1,
NM_003501.2,
Ensembl idENSG00000087008
DescriptionBRCACoxacyl-Coenzyme A oxidase 3, pristanoylbranched-chain acyl-CoA oxidaseperoxisomal acyl-coenzyme A oxidase 3pristanoyl-CoA oxidase
Modification date20141207
dbXrefs MIM : 603402
HGNC : HGNC
Ensembl : ENSG00000087008
HPRD : 04552
Vega : OTTHUMG00000090509
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACOX3
BioGPS: 8310
Gene Expression Atlas: ENSG00000087008
The Human Protein Atlas: ENSG00000087008
PathwayNCI Pathway Interaction Database: ACOX3
KEGG: ACOX3
REACTOME: ACOX3
ConsensusPathDB
Pathway Commons: ACOX3
MetabolismMetaCyc: ACOX3
HUMANCyc: ACOX3
RegulationEnsembl's Regulation: ENSG00000087008
miRBase: chr4 :8,368,008-8,442,452
TargetScan: NM_001101667
cisRED: ENSG00000087008
ContextiHOP: ACOX3
cancer metabolism search in PubMed: ACOX3
UCL Cancer Institute: ACOX3
Assigned class in ccmGDBC

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Phenotypic Information for ACOX3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACOX3
Familial Cancer Database: ACOX3
* 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_FATTY_ACID_METABOLISM
KEGG_ALPHA_LINOLENIC_ACID_METABOLISM
REACTOME_PEROXISOMAL_LIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ACOX3
MedGen: ACOX3 (Human Medical Genetics with Condition)
ClinVar: ACOX3
PhenotypeMGI: ACOX3 (International Mouse Phenotyping Consortium)
PhenomicDB: ACOX3

Mutations for ACOX3
* 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 ACOX3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI915466ACOX3164484423738442438DLGAP462839203512510735129000
AA527241ACOX31179483693208369498C1orf1061734911200875031200875352
BF990548ACOX31777484075328407592ACOX373115484110688411244

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      
LOSS (# sample)        1        
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=63)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=1)
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
chr4:8401309-8401309p.E283K3
chr4:8401339-8401339p.L273F3
chr4:8401376-8401376p.F260F3
chr4:8401327-8401327p.M277L2
chr4:8398737-8398737p.R328H2
chr4:8396360-8396360p.R389H2
chr4:8417620-8417620p.R84Q2
chr4:8401369-8401369p.F263V2
chr4:8368805-8368805p.L662L2
chr4:8398744-8398744p.A326T2

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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
# sample32 12    42 1151 1169 9
# mutation32 11    42 1151 11510 9
nonsynonymous SNV32 8    32 751 1116 8
synonymous SNV   4    1  4    44 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
chr4:8383332p.L273F,ACOX32
chr4:8396360p.K146K,ACOX32
chr4:8416596p.R389H,ACOX32
chr4:8401339p.A514T,ACOX32
chr4:8398744p.A326T,ACOX32
chr4:8383294p.T50T,ACOX31
chr4:8407736p.A669T1
chr4:8394092p.P446T,ACOX31
chr4:8416072p.A315V,ACOX31
chr4:8368786p.K194R,ACOX31

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 ACOX3 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 ACOX3

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

ACOX3,ADD1,TRMT44,CASZ1,BLOC1S4,GAK,HMGCL,
KIAA0232,CERS4,LETM1,MAN2B2,MRFAP1,MRFAP1L1,NUDT16L1,
PAFAH2,PIGG,RBM47,STX18,TADA2B,WDR1,WFS1
ACOX3,ARHGAP8,HID1,KDF1,CAPN13,CARD14,CCDC57,
DLG3,ESRP2,FAM110C,FAM174B,GPR39,KIAA0319L,PAFAH2,
PIGO,PRR15L,REEP6,SEC16A,SIDT1,STYK1,TMEM63C

ACOX3,TRMT44,C4orf48,BLOC1S4,CTBP1,DOK4,GAK,
HMGCL,HTT,KCNQ1,KIAA2013,LETM1,MAEA,PRKCZ,
STX18,TADA2B,TBC1D14,TNIP2,TST,WDR1,NELFA
ACOX3,SLC35F6,CAPN1,CYP4F22,DAO,GPT,IL2RB,
KIR2DL4,MOV10,MVP,PRKD2,PYCARD,RALY,SLC6A9,
SNORA72,STX4,TAPBP,TRIM14,TRIM26,TYMP,VPS16
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 ACOX3


There's no related Drug.
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Cross referenced IDs for ACOX3
* 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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