Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 ABCB4
Basic gene info.Gene symbolABCB4
Gene nameATP-binding cassette, sub-family B (MDR/TAP), member 4
SynonymsABC21|GBD1|ICP3|MDR2|MDR2/3|MDR3|PFIC-3|PGY3
CytomapUCSC genome browser: 7q21.1
Genomic locationchr7 :87031360-87105019
Type of geneprotein-coding
RefGenesNM_000443.3,
NM_018849.2,NM_018850.2,
Ensembl idENSG00000005471
DescriptionATP-binding cassette sub-family B member 4P glycoprotein 3/multiple drug resistance 3P-glycoprotein 3P-glycoprotein-3/multiple drug resistance-3multidrug resistance protein 3multiple drug resistance 3
Modification date20141207
dbXrefs MIM : 171060
HGNC : HGNC
Ensembl : ENSG00000005471
HPRD : 01371
Vega : OTTHUMG00000023396
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ABCB4
BioGPS: 5244
Gene Expression Atlas: ENSG00000005471
The Human Protein Atlas: ENSG00000005471
PathwayNCI Pathway Interaction Database: ABCB4
KEGG: ABCB4
REACTOME: ABCB4
ConsensusPathDB
Pathway Commons: ABCB4
MetabolismMetaCyc: ABCB4
HUMANCyc: ABCB4
RegulationEnsembl's Regulation: ENSG00000005471
miRBase: chr7 :87,031,360-87,105,019
TargetScan: NM_000443
cisRED: ENSG00000005471
ContextiHOP: ABCB4
cancer metabolism search in PubMed: ABCB4
UCL Cancer Institute: ABCB4
Assigned class in ccmGDBC

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Phenotypic Information for ABCB4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ABCB4
Familial Cancer Database: ABCB4
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ABCB4
MedGen: ABCB4 (Human Medical Genetics with Condition)
ClinVar: ABCB4
PhenotypeMGI: ABCB4 (International Mouse Phenotyping Consortium)
PhenomicDB: ABCB4

Mutations for ABCB4
* 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
ovaryABCB4chr78705890787058927chr7118123599118123619
pancreasABCB4chr78708666487086684ABCB4chr78708993387089953
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 ABCB4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1   111  
GAIN (# sample)        1   111  
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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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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=159)
Stat. for Synonymous SNVs
(# total SNVs=45)
Stat. for Deletions
(# total SNVs=12)
Stat. for Insertions
(# total SNVs=3)

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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
chr7:87074282-87074282p.S339fs*34
chr7:87101970-87101970p.T34T3
chr7:87043015-87043015p.E901*3
chr7:87031414-87031414p.*1280R3
chr7:87104707-87104707p.I25I3
chr7:87092091-87092091p.G90E3
chr7:87081113-87081113p.?2
chr7:87032470-87032470p.L1205P2
chr7:87038587-87038587p.L1016L2
chr7:87056076-87056076p.T685N2

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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
# sample45 218 9 3  23127121821120
# mutation45 238 10 3  26137122121134
nonsynonymous SNV32 165 7 2  20951 1317126
synonymous SNV13 73 3 1  642 284 8
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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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
chr7:87101970p.T34T,ABCB43
chr7:87069080p.L1158P,ABCB42
chr7:87069667p.L1158V,ABCB42
chr7:87092091p.G90E,ABCB42
chr7:87032470p.T685N,ABCB42
chr7:87032471p.E470K,ABCB42
chr7:87056076p.R545H,ABCB42
chr7:87035760p.R529R,ABCB41
chr7:87083895p.S1078N,ABCB41
chr7:87046828p.Q423Q,ABCB41

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 ABCB4 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 ABCB4

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))
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check002.gifCNV 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
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

ABCB4,ANGPTL3,APOB,ASGR2,BMP10,C9,CATSPER1,
CD22,CREB3L3,DBH,F2,FABP1,FGF23,ITIH1,
ITIH3,PLG,SERPINA7,SLC17A2,SPP2,TM4SF5,VTN
ABCB4,BIN1,CFL2,CLCN4,CLIC5,CLTCL1,COX7A1,
CUTC,DYSF,EYA4,FILIP1,FYCO1,IL17D,KCNJ12,
MEF2C,MN1,PHKG1,PPAPDC3,TMOD1,TUBA8,ZNF106

ABCB4,APCDD1,BBS5,C2orf57,GLP1R,GLUL,HRNR,
IGF2,INS-IGF2,KIAA0087,LOC92973,MPO,OR13J1,OR6B3,
ORAI2,RLBP1,SLAMF6,SLC14A1,SLC22A9,TMEM204,TRIL
ABCB1,ABCB4,ABCG1,C1orf106,C1orf115,C2CD2L,COBL,
DYRK2,GCOM1,HECA,IFNLR1,KCNK5,KIAA0247,LAMB3,
MALL,NR1I2,PIGS,PTK2B,SGK223,SLC9A3R1,TGOLN2
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

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check002.gifInteracting 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 ABCB4
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
DB00143ATP-binding cassette, sub-family B (MDR/TAP), member 4approved; nutraceuticalGlutathione
DB00997ATP-binding cassette, sub-family B (MDR/TAP), member 4approved; investigationalDoxorubicin
DB00382ATP-binding cassette, sub-family B (MDR/TAP), member 4approvedTacrine


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Cross referenced IDs for ABCB4
* 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



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