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 symbolABCA1
Gene nameATP-binding cassette, sub-family A (ABC1), member 1
CytomapUCSC genome browser: 9q31.1
Genomic locationchr9 :107543283-107690527
Type of geneprotein-coding
Ensembl idENSG00000165029
DescriptionATP-binding cassette sub-family A member 1ATP-binding cassette transporter A1cholesterol efflux regulatory proteinmembrane-bound
Modification date20141222
dbXrefs MIM : 600046
Ensembl : ENSG00000165029
HPRD : 02501
Vega : OTTHUMG00000020417
ProteinUniProt: O95477
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ABCA1
BioGPS: 19
Gene Expression Atlas: ENSG00000165029
The Human Protein Atlas: ENSG00000165029
PathwayNCI Pathway Interaction Database: ABCA1
Pathway Commons: ABCA1
MetabolismMetaCyc: ABCA1
RegulationEnsembl's Regulation: ENSG00000165029
miRBase: chr9 :107,543,283-107,690,527
TargetScan: NM_005502
cisRED: ENSG00000165029
ContextiHOP: ABCA1
cancer metabolism search in PubMed: ABCA1
UCL Cancer Institute: ABCA1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ABCA1 in cancer cell metabolism1. 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

Phenotypic Information for ABCA1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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;,
2 Tumor Suppressor gene;,
3 Cancer Gene Census;,
4 CancerGenes;,
5 Network of Cancer Gene;,
1Therapeutic Vulnerabilities in Cancer;

check002.gifMetabolic Pathway Description

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.
DiseaseKEGG Disease: ABCA1
MedGen: ABCA1 (Human Medical Genetics with Condition)
ClinVar: ABCA1
PhenotypeMGI: ABCA1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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.
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ABCA1 related fusion information.
IDHead GeneTail Gene

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample11               
GAIN (# sample) 1               
LOSS (# sample)1                
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)

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=6

check002.gifSomatic 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.

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

check002.gifSNV 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 ID1234567891011121314151617181920
# sample651407 9 81 18126  1217123
# mutation651507 9 81 25146  1218135
nonsynonymous SNV541385 6 71 1886  815128
synonymous SNV11 122 3 1  76   43 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])

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

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 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]

Gene Expression for ABCA1

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))
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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


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

check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Pharmacological Information for ABCA1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2362986; -.
ChemistryGuidetoPHARMACOLOGY 756; -.
ChemistryChEMBL CHEMBL2362986; -.
ChemistryGuidetoPHARMACOLOGY 756; -.
Organism-specific databasesPharmGKB PA24373; -.
Organism-specific databasesPharmGKB PA24373; -.
Organism-specific databasesCTD 19; -.
Organism-specific databasesCTD 19; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00171ATP-binding cassette, sub-family A (ABC1), member 1approved; nutraceuticalAdenosine triphosphate
DB01016ATP-binding cassette, sub-family A (ABC1), member 1approvedGlyburide
DB01599ATP-binding cassette, sub-family A (ABC1), member 1approvedProbucol
DB01039ATP-binding cassette, sub-family A (ABC1), member 1approvedFenofibrate
DB01076ATP-binding cassette, sub-family A (ABC1), member 1approvedAtorvastatin
DB00755ATP-binding cassette, sub-family A (ABC1), member 1approved; nutraceutical; investigationalTretinoin
DB01095ATP-binding cassette, sub-family A (ABC1), member 1approvedFluvastatin
DB00412ATP-binding cassette, sub-family A (ABC1), member 1approved; investigationalRosiglitazone
DB00264ATP-binding cassette, sub-family A (ABC1), member 1approved; investigationalMetoprolol

Cross referenced IDs for ABCA1
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories.

: Open all cross reference information

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