Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	ACO1
	Gene name	aconitase 1, soluble
	Synonyms	ACONS\|HEL60\|IREB1\|IREBP\|IREBP1\|IRP1
	Cytomap	UCSC genome browser: 9p21.1
	Genomic location	chr9 :32384600-32450832
	Type of gene	protein-coding
	RefGenes	NM_001278352.1, NM_002197.2,
	Ensembl id	ENSG00000122729
	Description	IRE-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 date	20141207
dbXrefs	MIM : 100880
	HGNC : HGNC
	Ensembl : ENSG00000122729
	HPRD : 00013
	Vega : OTTHUMG00000019740
Protein	UniProt: P21399 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ACO1
	BioGPS: 48
	Gene Expression Atlas: ENSG00000122729
	The Human Protein Atlas: ENSG00000122729
Pathway	NCI Pathway Interaction Database: ACO1
	KEGG: ACO1
	REACTOME: ACO1
	ConsensusPathDB
	Pathway Commons: ACO1
Metabolism	MetaCyc: ACO1
	HUMANCyc: ACO1
Regulation	Ensembl's Regulation: ENSG00000122729
	miRBase: chr9 :32,384,600-32,450,832
	TargetScan: NM_001278352
	cisRED: ENSG00000122729
Context	iHOP: ACO1
	cancer metabolism search in PubMed: ACO1
	UCL Cancer Institute: ACO1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ACO1 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM

Others
OMIM	100880; gene.
Orphanet
Disease	KEGG Disease: ACO1
	MedGen: ACO1 (Human Medical Genetics with Condition)
	ClinVar: ACO1
Phenotype	MGI: ACO1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ACO1 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
AA572951	ACO1	7	97	9	32416358	32416448	ACO1	93	605	9	32416441	32416953
BQ350502	ACO1	12	158	9	32420969	32423408	ACO1	154	679	9	32418128	32420990

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr9:32418371-32418371	p.S174T	3
chr9:32450052-32450052	p.L871L	3
chr9:32425989-32425989	p.G448R	2
chr9:32407360-32407360	p.N67D	2
chr9:32407428-32407428	p.?	2
chr9:32427421-32427421	p.L491L	2
chr9:32424622-32424622	p.S383A	2
chr9:32418455-32418455	p.V202M	2
chr9:32405519-32405519	p.F5F	2
chr9:32425910-32425910	p.E421E	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2	3	2	9	1		5		6	1		6	2	1	1		5	7		21
# mutation	2	3	2	11	1		6		6	1		6	2	1	1		4	8		25
nonsynonymous SNV	1	2	2	9	1		6		5	1		4	2	1	1		2	7		15
synonymous SNV	1	1		2					1			2					2	1		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr9:32419040	p.V202M,ACO1	2
chr9:32425989	p.V221V,ACO1	2
chr9:32424622	p.S383P,ACO1	2
chr9:32405519	p.F5F,ACO1	2
chr9:32418455	p.S38L,ACO1	2
chr9:32407274	p.G448R,ACO1	2
chr9:32431799	p.A687T,ACO1	1
chr9:32423350	p.N807Y,ACO1	1
chr9:32436252	p.P111T,ACO1	1
chr9:32407405	p.V321A,ACO1	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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