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 ACO2

Basic gene info.	Gene symbol	ACO2
	Gene name	aconitase 2, mitochondrial
	Synonyms	ACONM\|ICRD
	Cytomap	UCSC genome browser: 22q13.2
	Genomic location	chr22 :41865128-41924993
	Type of gene	protein-coding
	RefGenes	NM_001098.2,
	Ensembl id	ENSG00000100412
	Description	aconitate hydratase, mitochondrialcitrate hydro-lyase
	Modification date	20141207
dbXrefs	MIM : 100850
	HGNC : HGNC
	Ensembl : ENSG00000100412
	HPRD : 00012
	Vega : OTTHUMG00000030544
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ACO2
	BioGPS: 50
	Gene Expression Atlas: ENSG00000100412
	The Human Protein Atlas: ENSG00000100412
Pathway	NCI Pathway Interaction Database: ACO2
	KEGG: ACO2
	REACTOME: ACO2
	ConsensusPathDB
	Pathway Commons: ACO2
Metabolism	MetaCyc: ACO2
	HUMANCyc: ACO2
Regulation	Ensembl's Regulation: ENSG00000100412
	miRBase: chr22 :41,865,128-41,924,993
	TargetScan: NM_001098
	cisRED: ENSG00000100412
Context	iHOP: ACO2
	cancer metabolism search in PubMed: ACO2
	UCL Cancer Institute: ACO2
Assigned class in ccmGDB	C

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Phenotypic Information for ACO2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ACO2
	Familial Cancer Database: ACO2

* 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/

Metabolic Pathway Description
KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: ACO2
	MedGen: ACO2 (Human Medical Genetics with Condition)
	ClinVar: ACO2
Phenotype	MGI: ACO2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ACO2

Mutations for ACO2

* 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

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	ACO2	chr22	41878753	41878773	ZC3H7B	chr22	41740739	41740759

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ACO2 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
DA891854	ACTB	1	332	7	5568907	5570232	ACO2	331	486	22	41903933	41907914
DA577703	SURF4	1	96	9	136242836	136242931	ACO2	91	574	22	41921254	41923965
CV352271	CDK20	1	251	9	90582462	90584246	ACO2	238	473	22	41903923	41923971
AW379928	ACO2	22	88	22	41903912	41903979	EZR	81	591	6	159236148	159236652
BU849679	TOB2	1	403	22	41842383	41842785	ACO2	404	795	22	41895730	41904048
BI000114	COG7	1	316	16	23434484	23434797	ACO2	303	512	22	41919719	41919928
BI596363	ANK2	6	185	4	114038165	114038344	ACO2	185	648	22	41911472	41916222

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

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

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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=45)	Stat. for Synonymous SNVs (# total SNVs=17)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

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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
chr22:41918875-41918875	p.G394R	2
chr22:41895860-41895860	p.R56H	2
chr22:41924477-41924477	p.?	2
chr22:41922274-41922274	p.G590G	2
chr22:41913580-41913580	p.S295S	2
chr22:41911475-41911475	p.G207V	2
chr22:41903940-41903940	p.M107V	2
chr22:41924552-41924552	p.E760K	2
chr22:41911525-41911525	p.L224L	2
chr22:41923335-41923335	p.G666D	1

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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	5	4		4			3		1			4	3	1			8	9		9
# mutation	5	4		4			3		1			4	3	1			8	9		12
nonsynonymous SNV	2	3		3			2					1	3	1			4	5		7
synonymous SNV	3	1		1			1		1			3					4	4		5

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
chr22:41913580	p.S295S	2
chr22:41903905	p.R656R	1
chr22:41921257	p.E149D	1
chr22:41911921	p.D430E	1
chr22:41924005	p.G666G	1
chr22:41919217	p.N152T	1
chr22:41903923	p.G431R	1
chr22:41922335	p.S669S	1
chr22:41924017	p.P168T	1
chr22:41919867	p.I435I	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 ACO2 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 ACO2

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


ACO2,ANKRD54,AP1B1,RTCB,ST13P4,L3MBTL2,MCAT, NDUFA6,NHP2L1,PHF5A,PMM1,POLDIP3,POLR3H,RANGAP1, SAMM50,SLC25A17,SREBF2,ST13,TOMM22,TXN2,XRCC6	ACAT1,ACO2,ALPK3,ATP5B,ADCK3,CDK16,CHCHD10, CHCHD3,FH,GYS1,IMMT,MLYCD,NDUFS1,OGDH, PGM1,RAD23A,RXRG,SDHA,SDHB,SNTA1,UQCRFS1

ACO2,ATP5B,RTCB,CHCHD10,CPT2,DDT,DEPDC5, FAM83F,GOT1,L3MBTL2,NDUFA6,PXMP2,SAMM50,SDHA, SH3BP1,SLC5A1,SREBF2,TTLL12,TXN2,UQCR10,UQCRC1	ACO2,AGPAT3,ANKS4B,ANO10,CES2,CLPTM1,CRAT, DCAF11,DHRS11,GDPD2,GNA11,HADHA,KCNK5,LAMB3, MGAT4B,NGEF,PIGS,PNPLA6,POR,USH1C,VIL1

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 ACO2

There's no related Drug.

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Cross referenced IDs for ACO2

* 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