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 ABCA1

Basic gene info.	Gene symbol	ABCA1
	Gene name	ATP-binding cassette, sub-family A (ABC1), member 1
	Synonyms	ABC-1\|ABC1\|CERP\|HDLDT1\|TGD
	Cytomap	UCSC genome browser: 9q31.1
	Genomic location	chr9 :107543283-107690527
	Type of gene	protein-coding
	RefGenes	NM_005502.3,
	Ensembl id	ENSG00000165029
	Description	ATP-binding cassette sub-family A member 1ATP-binding cassette transporter A1cholesterol efflux regulatory proteinmembrane-bound
	Modification date	20141222
dbXrefs	MIM : 600046
	HGNC : HGNC
	Ensembl : ENSG00000165029
	HPRD : 02501
	Vega : OTTHUMG00000020417
Protein	UniProt: O95477 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ABCA1
	BioGPS: 19
	Gene Expression Atlas: ENSG00000165029
	The Human Protein Atlas: ENSG00000165029
Pathway	NCI Pathway Interaction Database: ABCA1
	KEGG: ABCA1
	REACTOME: ABCA1
	ConsensusPathDB
	Pathway Commons: ABCA1
Metabolism	MetaCyc: ABCA1
	HUMANCyc: ABCA1
Regulation	Ensembl's Regulation: ENSG00000165029
	miRBase: chr9 :107,543,283-107,690,527
	TargetScan: NM_005502
	cisRED: ENSG00000165029
Context	iHOP: ABCA1
	cancer metabolism search in PubMed: ABCA1
	UCL Cancer Institute: ABCA1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ABCA1 in cancer cell metabolism	1. Lee BH, Taylor MG, Robinet P, Smith JD, Schweitzer J, et al. (2013) Dysregulation of cholesterol homeostasis in human prostate cancer through loss of ABCA1. Cancer Res 73: 1211-1218. doi: 10.1158/0008-5472.CAN-12-3128. pmid: 3563867 go to article 2. He Y, Zhang L, Li Z, Gao H, Yue Z, et al. (2015) RIP140 triggers foam-cell formation by repressing ABCA1/G1 expression and cholesterol efflux via liver X receptor. FEBS Lett 589: 455-460. doi: 10.1016/j.febslet.2015.01.001. go to article 3. Vargas T, Moreno-Rubio J, Herranz J, Cejas P, Molina S, et al. (2015) ColoLipidGene: signature of lipid metabolism-related genes to predict prognosis in stage-II colon cancer patients. Oncotarget 6: 7348-7363. pmid: 4466690. go to article 4. Smith B, Land H (2012) Anticancer activity of the cholesterol exporter ABCA1 gene. Cell Rep 2: 580-590. doi: 10.1016/j.celrep.2012.08.011. pmid: 3462268. go to article 5. Jones RJ, Gu D, Bjorklund CC, Kuiatse I, Remaley AT, et al. (2013) The novel anticancer agent JNJ-26854165 induces cell death through inhibition of cholesterol transport and degradation of ABCA1. J Pharmacol Exp Ther 346: 381-392. doi: 10.1124/jpet.113.204958. pmid: 3876782. go to article

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Phenotypic Information for ABCA1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ABCA1
	Familial Cancer Database: ABCA1

* 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
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS REACTOME_LIPOPROTEIN_METABOLISM

Others
OMIM	205400; phenotype. 205400; phenotype. 600046; gene+phenotype. 600046; gene+phenotype. 604091; phenotype. 604091; phenotype.
Orphanet	31150; Tangier disease. 31150; Tangier disease. 425; Apolipoprotein A-I deficiency. 425; Apolipoprotein A-I deficiency.
Disease	KEGG Disease: ABCA1
	MedGen: ABCA1 (Human Medical Genetics with Condition)
	ClinVar: ABCA1
Phenotype	MGI: ABCA1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ABCA1

Mutations for ABCA1

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	ABCA1	chr9	107666329	107666349	BRAF	chr7	140485456	140485476

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 ABCA1 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
AK130814	ABCA1	14	1438	9	107576733	107588168	LAS1L	1434	1987	X	64732463	64737950
BF879888	ABCA1	7	294	9	107587996	107589344	EIF4E	288	486	4	99809803	99810001
DB286350	ABCA1	1	381	9	107665894	107690436	KCNMA1	381	462	10	78850187	78850268
CR983438	ABCA1	1	190	9	107690215	107690404	HNRNPK	188	858	9	86587842	86593369
BF988288	SNRNP200	1	188	2	96966780	96967435	ABCA1	181	466	9	107639717	107640002

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=199)	Stat. for Synonymous SNVs (# total SNVs=60)

Stat. for Deletions (# total SNVs=4)	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
chr9:107571802-107571802	p.A1407T	5
chr9:107588035-107588035	p.S824L	4
chr9:107602666-107602666	p.G316G	4
chr9:107624029-107624029	p.L158L	4
chr9:107556793-107556793	p.?	3
chr9:107571749-107571749	p.I1424I	3
chr9:107620867-107620867	p.R219K	3
chr9:107620894-107620894	p.E210G	2
chr9:107581161-107581161	p.R1082H	2
chr9:107573173-107573173	p.A1361A	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	6	5	1	40	7		9		8	1		18	12	6			12	17	1	23
# mutation	6	5	1	50	7		9		8	1		25	14	6			12	18	1	35
nonsynonymous SNV	5	4	1	38	5		6		7	1		18	8	6			8	15	1	28
synonymous SNV	1	1		12	2		3		1			7	6				4	3		7

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
chr9:107571802	p.S824L	3
chr9:107588035	p.A1407T	3
chr9:107583698	p.G1502E	2
chr9:107645350	p.S2192N	2
chr9:107566961	p.E210G	2
chr9:107645364	p.V2098V	2
chr9:107547747	p.L1232L	2
chr9:107584854	p.P1547A	2
chr9:107578466	p.T131S	2
chr9:107594877	p.Q973R	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 ABCA1 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 ABCA1

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


ABCA1,DOCK11,DOCK4,HEG1,KCTD12,KIAA1033,LEPROT, LHFPL2,MARCH1,MSR1,PCNX,PLXNC1,RAB8B,SETX, PEAK1,SGTB,SLC8A1,SSH1,TLR4,ZEB2,ZNF699	ABCA1,ABCC9,ANO6,ANTXR2,AQPEP,CD36,CDO1, CELF2,COL4A3BP,CPM,DIAPH2,EBF1,FRMD4A,GHR, GNAI1,JAK1,LAMC1,TENM3___TENM1,PDE8A,RHOBTB3,ZEB2

ABCA1,ARHGEF6,ATP8B4,CYP7B1,DDR2,FBN1,FLI1, GNB4,HEG1,IL1R1,IL6ST,MAF,MYO5A,NR3C1, NRP1,PKD2,QKI,STAB1,STARD8,TLR1,ZEB2	A2M,ABCA1,ARNT,COL4A3BP,FZD1,GIMAP8,GPNMB, HAP1,KDR,LOC283999,LTBP2,PCDH12,PLXND1,RASA3, RRAGD,SLC23A2,SMG6,SRGAP3,TLE4,UBE4B,WASF2

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 ABCA1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL2362986; -.
Chemistry	GuidetoPHARMACOLOGY	756; -.
Chemistry	ChEMBL	CHEMBL2362986; -.
Chemistry	GuidetoPHARMACOLOGY	756; -.
Organism-specific databases	PharmGKB	PA24373; -.
Organism-specific databases	PharmGKB	PA24373; -.
Organism-specific databases	CTD	19; -.
Organism-specific databases	CTD	19; -.

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
DB00171	ATP-binding cassette, sub-family A (ABC1), member 1	approved; nutraceutical	Adenosine triphosphate
DB01016	ATP-binding cassette, sub-family A (ABC1), member 1	approved	Glyburide
DB01599	ATP-binding cassette, sub-family A (ABC1), member 1	approved	Probucol
DB01039	ATP-binding cassette, sub-family A (ABC1), member 1	approved	Fenofibrate
DB01076	ATP-binding cassette, sub-family A (ABC1), member 1	approved	Atorvastatin
DB00755	ATP-binding cassette, sub-family A (ABC1), member 1	approved; nutraceutical; investigational	Tretinoin
DB01095	ATP-binding cassette, sub-family A (ABC1), member 1	approved	Fluvastatin
DB00412	ATP-binding cassette, sub-family A (ABC1), member 1	approved; investigational	Rosiglitazone
DB00264	ATP-binding cassette, sub-family A (ABC1), member 1	approved; investigational	Metoprolol

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Cross referenced IDs for ABCA1

* 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