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 ACACB

Basic gene info.	Gene symbol	ACACB
	Gene name	acetyl-CoA carboxylase beta
	Synonyms	ACC2\|ACCB\|HACC275
	Cytomap	UCSC genome browser: 12q24.11
	Genomic location	chr12 :109577201-109706030
	Type of gene	protein-coding
	RefGenes	NM_001093.3,
	Ensembl id	ENSG00000076555
	Description	ACC-betaacetyl-CoA carboxylase 2acetyl-Coenzyme A carboxylase beta
	Modification date	20141207
dbXrefs	MIM : 601557
	HGNC : HGNC
	Ensembl : ENSG00000076555
	HPRD : 07044
	Vega : OTTHUMG00000169250
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ACACB
	BioGPS: 32
	Gene Expression Atlas: ENSG00000076555
	The Human Protein Atlas: ENSG00000076555
Pathway	NCI Pathway Interaction Database: ACACB
	KEGG: ACACB
	REACTOME: ACACB
	ConsensusPathDB
	Pathway Commons: ACACB
Metabolism	MetaCyc: ACACB
	HUMANCyc: ACACB
Regulation	Ensembl's Regulation: ENSG00000076555
	miRBase: chr12 :109,577,201-109,706,030
	TargetScan: NM_001093
	cisRED: ENSG00000076555
Context	iHOP: ACACB
	cancer metabolism search in PubMed: ACACB
	UCL Cancer Institute: ACACB
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: ACACB
	Familial Cancer Database: ACACB

* 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_PYRUVATE_METABOLISM KEGG_PROPANOATE_METABOLISM REACTOME_INTEGRATION_OF_ENERGY_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

Mutations for ACACB

* 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
ovary	ACACB	chr12	109612529	109612729		chr12	109163338	109163538
pancreas	ACACB	chr12	109605366	109605386	ACACB	chr12	109605598	109605618

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 ACACB 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
BM989099	ACACB	16	143	12	109705904	109706031	CTDSP1	144	435	2	219270373	219270664
BF375856	PANK2	105	228	20	3873479	3873602	ACACB	211	392	12	109625921	109629547
BF822123	ACACB	1	105	12	109626548	109626653	ACACB	101	398	12	109626532	109627157

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=207)	Stat. for Synonymous SNVs (# total SNVs=74)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=1)

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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
chr12:109613968-109613968	p.R446I	4
chr12:109702924-109702924	p.E2318*	3
chr12:109617881-109617881	p.A603T	3
chr12:109625967-109625967	p.S715L	3
chr12:109605836-109605836	p.A308P	3
chr12:109610082-109610082	p.A346A	2
chr12:109660682-109660682	p.M1253V	2
chr12:109687895-109687895	p.V1926F	2
chr12:109644522-109644522	p.P974L	2
chr12:109696853-109696853	p.R2146W	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=4

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	7	9	2	35	8		15		6	1		24	11	7		1	24	20	2	28
# mutation	6	9	2	37	8		19		6	1		34	14	7		1	29	29	2	46
nonsynonymous SNV	4	8	2	32	7		11		4			18	7	6		1	16	21	1	29
synonymous SNV	2	1		5	1		8		2	1		16	7	1			13	8	1	17

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
chr12:109613968	p.R89K	3
chr12:109577476	p.R446I	3
chr12:109660704	p.G1124S	2
chr12:109629448	p.P2188P	2
chr12:109654442	p.L826F	2
chr12:109680382	p.V320I	2
chr12:109631529	p.M1253V	2
chr12:109614053	p.P474P	2
chr12:109675151	p.P1721P	2
chr12:109623543	p.M1253I	2

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 ACACB 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 ACACB

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


ACACB,ACVR1C,ADH1B,ADIPOQ,AOC3,AQP7,AQP7P1, C14orf180,CD300LG,CIDEC,GPAM,GPD1,HEPACAM,KCNIP2, KLB,LIPE,PLIN1,PLIN4,SDPR,SLC19A3,TMEM132C	ABHD15,ACAA2,ACACB,ACVR1C,AQP7,CIDEC,CNTFR, GYG2,LGALS12,MLXIPL,MARC1,OXCT1,PC,PDE1B, PECR,PLA2G16,PNPLA2,PPARG,SLC19A3,TJP2,TMEM132C

ABCA6,ABCA8,ABCA9,ACACB,ADH1B,AQP7,C7, CD300LG,CIDEA,FABP4,GPIHBP1,GPX3,HEPACAM,KCNIP2, LIFR,NGFR,PLIN1,PLIN4,SCN4A,SEMA3G,TUSC5	ABCA3,ACACB,AHNAK,COL6A2,CROCCP3,DLG5,EVC, FYCO1,GLI2,IGHMBP2,CTIF,MTCL1,LAMA5,LAMB2, MACF1,MECP2,PKD1,SSC5D,SYNE1,ZFYVE20,ZNF512B

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 ACACB

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00121	acetyl-CoA carboxylase beta	approved; nutraceutical	Biotin
DB00173	acetyl-CoA carboxylase beta	approved; nutraceutical	Adenine
DB02859	acetyl-CoA carboxylase beta	experimental	Soraphen A
DB03781	acetyl-CoA carboxylase beta	experimental	2-[4-(2,4-Dichlorophenoxy)Phenoxy]Propanoic Acid
DB07870	acetyl-CoA carboxylase beta	experimental	(2S)-2-(4-{[3-CHLORO-5-(TRIFLUOROMETHYL)PYRIDIN-2-YL]OXY}PHENOXY)PROPANOIC ACID

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Cross referenced IDs for ACACB

* 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