Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 ABCG1
Basic gene info.Gene symbolABCG1
Gene nameATP-binding cassette, sub-family G (WHITE), member 1
SynonymsABC8|WHITE1
CytomapUCSC genome browser: 21q22.3
Genomic locationchr21 :43636186-43717354
Type of geneprotein-coding
RefGenesNM_004915.3,
NM_016818.2,NM_207174.1,NM_207627.1,NM_207628.1,
NM_207629.1,NM_207630.1,
Ensembl idENSG00000160179
DescriptionABC transporter 8ATP-binding cassette sub-family G member 1ATP-binding cassette transporter 8ATP-binding cassette transporter member 1 of subfamily Ghomolog of Drosophila whitewhite protein homolog (ATP-binding cassette transporter 8)
Modification date20141207
dbXrefs MIM : 603076
HGNC : HGNC
Ensembl : ENSG00000160179
HPRD : 04355
Vega : OTTHUMG00000086791
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ABCG1
BioGPS: 9619
Gene Expression Atlas: ENSG00000160179
The Human Protein Atlas: ENSG00000160179
PathwayNCI Pathway Interaction Database: ABCG1
KEGG: ABCG1
REACTOME: ABCG1
ConsensusPathDB
Pathway Commons: ABCG1
MetabolismMetaCyc: ABCG1
HUMANCyc: ABCG1
RegulationEnsembl's Regulation: ENSG00000160179
miRBase: chr21 :43,636,186-43,717,354
TargetScan: NM_004915
cisRED: ENSG00000160179
ContextiHOP: ABCG1
cancer metabolism search in PubMed: ABCG1
UCL Cancer Institute: ABCG1
Assigned class in ccmGDBC

Top
Phenotypic Information for ABCG1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ABCG1
Familial Cancer Database: ABCG1
* 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS
REACTOME_LIPOPROTEIN_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ABCG1
MedGen: ABCG1 (Human Medical Genetics with Condition)
ClinVar: ABCG1
PhenotypeMGI: ABCG1 (International Mouse Phenotyping Consortium)
PhenomicDB: ABCG1

Mutations for ABCG1
* 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
There's no inter-chromosomal structural variation.
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryABCG1chr214369693443696954ABCG1chr214369226743692287
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 ABCG1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
U34919ACSBG18354157852156278521908ABCG13542745214364583543716951

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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1  1 12 1        
GAIN (# sample)1                
LOSS (# sample)   1 12 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)

Top
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=4

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=51)
Stat. for Synonymous SNVs
(# total SNVs=27)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
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
chr21:43716283-43716283p.F606F3
chr21:43714663-43714663p.F567F2
chr21:43702433-43702433p.R213Q2
chr21:43708133-43708133p.R370W2
chr21:43710219-43710219p.L440L2
chr21:43711654-43711654p.S526L2
chr21:43691267-43691267p.S125Y2
chr21:43710232-43710232p.G445R2
chr21:43645875-43645875p.T46M2
chr21:43691291-43691291p.G133V2

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample23 123 3 3  713 1218 12
# mutation23 123 3 3  713 1219 15
nonsynonymous SNV22 72 3 3  312 1108 12
synonymous SNV 1 51      4 1  111 3
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])

Top
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
chr21:43716283p.F606F,ABCG13
chr21:43645875p.E22E,ABCG12
chr21:43708058p.T46M,ABCG12
chr21:43711712p.L440L,ABCG12
chr21:43710219p.F240F,ABCG12
chr21:43702515p.R345R,ABCG12
chr21:43645804p.G445R,ABCG12
chr21:43710232p.S545S,ABCG12
chr21:43702403p.G552G,ABCG11
chr21:43708138p.G3E1

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 ABCG1 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]

Top
Gene Expression for ABCG1

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

: Open all plots for all cancer types


Top
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

ABCG1,ACVR1B,ARF3,ASB8,CNNM3,DCAF11,ERBB3,
ERGIC1,FOXA1,GPR160,MARVELD2,MOAP1,MYLIP,PPM1A,
RAB19,RAB5B,SEPSECS,TADA2B,TBC1D9,TMEM30B,ZSWIM5
ABCG1,AKR1B1,C12orf75,CFAP61,CARM1,CCR3,DNASE1L1,
DOK5,DYSF,GMPR,IL17D,IL32,KCNJ12,PKM,
SCN1B,SH2B2,SLC16A3,SPAM1,TEAD4,TNNI3,TPI1

ABCG1,ACOX1,ACVRL1,BCAS1,CACFD1,CCNG2,CDHR5,
CEACAM1,CEACAM5,ITFG1,KIAA0513,LITAF,MGLL,OCEL1,
PIK3IP1,PRKCD,PTGER4,RNF103,SEPP1,SORL1,TMEM127
ABCG1,ABHD12,AMFR,C1orf106,C1orf115,FAM102A,GDPD2,
IL22RA1,KIAA0247,LASP1,LOC151534,MALL,PC,PDLIM1,
PIGS,POR,PTK2B,SCIN,SLC9A3R1,TMEM82,TOM1
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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for ABCG1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

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 G (WHITE), member 1approved; nutraceuticalAdenosine triphosphate
DB00762ATP-binding cassette, sub-family G (WHITE), member 1approved; investigationalIrinotecan


Top
Cross referenced IDs for ABCG1
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas