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 ACO1
Basic gene info.Gene symbolACO1
Gene nameaconitase 1, soluble
SynonymsACONS|HEL60|IREB1|IREBP|IREBP1|IRP1
CytomapUCSC genome browser: 9p21.1
Genomic locationchr9 :32384600-32450832
Type of geneprotein-coding
RefGenesNM_001278352.1,
NM_002197.2,
Ensembl idENSG00000122729
DescriptionIRE-BP 1aconitate hydratase, cytoplasmiccitrate hydro-lyasecytoplasmic aconitate hydrataseepididymis luminal protein 60ferritin repressor proteiniron regulatory protein 1iron-responsive element binding protein 1iron-responsive element-binding prot
Modification date20141207
dbXrefs MIM : 100880
HGNC : HGNC
Ensembl : ENSG00000122729
HPRD : 00013
Vega : OTTHUMG00000019740
ProteinUniProt: P21399
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACO1
BioGPS: 48
Gene Expression Atlas: ENSG00000122729
The Human Protein Atlas: ENSG00000122729
PathwayNCI Pathway Interaction Database: ACO1
KEGG: ACO1
REACTOME: ACO1
ConsensusPathDB
Pathway Commons: ACO1
MetabolismMetaCyc: ACO1
HUMANCyc: ACO1
RegulationEnsembl's Regulation: ENSG00000122729
miRBase: chr9 :32,384,600-32,450,832
TargetScan: NM_001278352
cisRED: ENSG00000122729
ContextiHOP: ACO1
cancer metabolism search in PubMed: ACO1
UCL Cancer Institute: ACO1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ACO1 in cancer cell metabolism1. Wang W, Deng Z, Hatcher H, Miller LD, Di X, et al. (2014) IRP2 regulates breast tumor growth. Cancer Res 74: 497-507. doi: 10.1158/0008-5472.CAN-13-1224. pmid: 3989290. go to article
2. Chen G, Fillebeen C, Wang J, Pantopoulos K (2007) Overexpression of iron regulatory protein 1 suppresses growth of tumor xenografts. Carcinogenesis 28: 785-791. doi: 10.1093/carcin/bgl210. pmid: 2925110. go to article
3. Haro KJ, Sheth A, Scheinberg DA (2012) Dysregulation of IRP1-mediated iron metabolism causes gamma ray-specific radioresistance in leukemia cells. PLoS One 7: e48841. doi: 10.1371/journal.pone.0048841. pmid: 3498264. go to article
4. Jeong SM, Lee J, Finley LW, Schmidt PJ, Fleming MD, et al. (2015) SIRT3 regulates cellular iron metabolism and cancer growth by repressing iron regulatory protein 1. Oncogene 34: 2115-2124. doi: 10.1038/onc.2014.124. go to article
5. Tong WH, Sourbier C, Kovtunovych G, Jeong SY, Vira M, et al. (2011) The glycolytic shift in fumarate-hydratase-deficient kidney cancer lowers AMPK levels, increases anabolic propensities and lowers cellular iron levels. Cancer Cell 20: 315-327. doi: 10.1016/j.ccr.2011.07.018. pmid: 3174047 go to article

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Phenotypic Information for ACO1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACO1
Familial Cancer Database: ACO1
* 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 MEL 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM

check002.gifOthers
OMIM 100880; gene.
Orphanet
DiseaseKEGG Disease: ACO1
MedGen: ACO1 (Human Medical Genetics with Condition)
ClinVar: ACO1
PhenotypeMGI: ACO1 (International Mouse Phenotyping Consortium)
PhenomicDB: ACO1

Mutations for ACO1
* 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 ACO1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA572951ACO179793241635832416448ACO19360593241644132416953
BQ350502ACO11215893242096932423408ACO115467993241812832420990

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 3           11  
GAIN (# sample)              1  
LOSS (# sample) 3           11  
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=61)
Stat. for Synonymous SNVs
(# total SNVs=20)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=2)

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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
chr9:32450052-32450052p.L871L3
chr9:32418371-32418371p.S174T3
chr9:32424622-32424622p.S383A2
chr9:32418455-32418455p.V202M2
chr9:32405519-32405519p.F5F2
chr9:32425910-32425910p.E421E2
chr9:32419040-32419040p.V221V2
chr9:32407274-32407274p.S38L2
chr9:32425989-32425989p.G448R2
chr9:32407360-32407360p.N67D2

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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
# sample23291 5 61 6211 57 21
# mutation232111 6 61 6211 48 25
nonsynonymous SNV12291 6 51 4211 27 15
synonymous SNV11 2    1  2    21 10
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
chr9:32424622p.V202M,ACO12
chr9:32405519p.V221V,ACO12
chr9:32418455p.S383P,ACO12
chr9:32407274p.F5F,ACO12
chr9:32419040p.S38L,ACO12
chr9:32425989p.G448R,ACO12
chr9:32423392p.T702T,ACO11
chr9:32436296p.G831W,ACO11
chr9:32408612p.L157V,ACO11
chr9:32430435p.R344Q,ACO11

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 ACO1 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 ACO1

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

ACO1,ACVR1C,ADH1A,ADH1B,ADIPOQ,ANTXR2,AOC3,
AQP7,AQPEP,GPAM,GPD1,GPX3,HSPB6,LGALS12,
MRAP,NPR1,NRP1,PLIN1,SLC19A3,TNS1,ZEB2
ACO1,ALDH2,AOC3,FAM213A,CALB2,CAT,CIDEC,
ESYT1,FERMT2,GPD1,GYG2,HEPACAM,HEPN1,HRASLS5,
LIPE,MARC1,MRAS,PLIN1,SIK2,TSPAN3,TYRO3

ACO1,ALDH6A1,ALDH9A1,C9orf152,CDC37L1,CEP70,DCAF12,
GNAQ,GOLPH3L,GRHPR,HADHB,KIAA0368,LOC100129034,NNT,
PIGR,SMARCA2,SMU1,TMEM8B,TTC39B,VCP,VWA5A
ACO1,AHCYL1,LINC01555,CPPED1,CREB3L2,EXOC6B,GNS,
GPI,HOXC5,HOXC6,HSD3B7,ICMT,LONP2,MEGF9,
NBAS,NFIB,REG3G,SMC3,TGM2,PRSS58,VPS35
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 ACO1


There's no related Drug.
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Cross referenced IDs for ACO1
* 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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