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 ABCB11
Basic gene info.Gene symbolABCB11
Gene nameATP-binding cassette, sub-family B (MDR/TAP), member 11
SynonymsABC16|BRIC2|BSEP|PFIC-2|PFIC2|PGY4|SPGP
CytomapUCSC genome browser: 2q24
Genomic locationchr2 :169779448-169887833
Type of geneprotein-coding
RefGenesNM_003742.2,
Ensembl idENSG00000263298
DescriptionABC member 16, MDR/TAP subfamilyATP-binding cassette sub-family B member 11bile salt export pumpprogressive familial intrahepatic cholestasis 2sister p-glycoprotein
Modification date20141207
dbXrefs MIM : 603201
HGNC : HGNC
Ensembl : ENSG00000073734
HPRD : 04436
Vega : OTTHUMG00000154039
ProteinUniProt: O95342
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ABCB11
BioGPS: 8647
Gene Expression Atlas: ENSG00000263298
The Human Protein Atlas: ENSG00000263298
PathwayNCI Pathway Interaction Database: ABCB11
KEGG: ABCB11
REACTOME: ABCB11
ConsensusPathDB
Pathway Commons: ABCB11
MetabolismMetaCyc: ABCB11
HUMANCyc: ABCB11
RegulationEnsembl's Regulation: ENSG00000263298
miRBase: chr2 :169,779,448-169,887,833
TargetScan: NM_003742
cisRED: ENSG00000263298
ContextiHOP: ABCB11
cancer metabolism search in PubMed: ABCB11
UCL Cancer Institute: ABCB11
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ABCB11 in cancer cell metabolism1. Homolya L, Fu D, Sengupta P, Jarnik M, Gillet JP, et al. (2014) LKB1/AMPK and PKA control ABCB11 trafficking and polarization in hepatocytes. PLoS One 9: e91921. doi: 10.1371/journal.pone.0091921. pmid: 3958433. go to article
2. Hlavata I, Mohelnikova-Duchonova B, Vaclavikova R, Liska V, Pitule P, et al. (2012) The role of ABC transporters in progression and clinical outcome of colorectal cancer. Mutagenesis 27: 187-196. doi: 10.1093/mutage/ger075. go to article

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Phenotypic Information for ABCB11(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ABCB11
Familial Cancer Database: ABCB11
* 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 601847; phenotype.
603201; gene.
605479; phenotype.
Orphanet 69665; Intrahepatic cholestasis of pregnancy.
79304; Progressive familial intrahepatic cholestasis type 2.
99961; Benign recurrent intrahepatic cholestasis type 2.
DiseaseKEGG Disease: ABCB11
MedGen: ABCB11 (Human Medical Genetics with Condition)
ClinVar: ABCB11
PhenotypeMGI: ABCB11 (International Mouse Phenotyping Consortium)
PhenomicDB: ABCB11

Mutations for ABCB11
* 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
pancreasABCB11chr2169800247169800267NOSTRINchr2169719372169719392
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 ABCB11 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA984265SRP141141154033108540331369ABCB111424582169869119169869435

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 # sample61 1    5 4 3   5
GAIN (# sample)21      4 4 2   3
LOSS (# sample)4  1    1   1   2
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=122)
Stat. for Synonymous SNVs
(# total SNVs=35)
Stat. for Deletions
(# total SNVs=5)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr2:169780250-169780250p.A1283V4
chr2:169814479-169814479p.L780I4
chr2:169828491-169828491p.E502Q2
chr2:169847412-169847412p.Y269Y2
chr2:169781166-169781166p.?2
chr2:169842673-169842673p.G344S2
chr2:169787307-169787307p.S1093S2
chr2:169783815-169783815p.G1157R2
chr2:169851889-169851889p.S194*2
chr2:169869891-169869891p.D94H2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 6 224 7 3 12472  3311115
# mutation 6 274 9 3 12772  4713120
nonsynonymous SNV 5 202 6 3 11862  3310115
synonymous SNV 1 72 3    91   143 5
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
chr2:169814479p.D94N2
chr2:169842636p.Q1215H2
chr2:169842673p.G1267S2
chr2:169780299p.P356Q2
chr2:169781287p.G344S2
chr2:169869891p.L780V2
chr2:169824975p.I891I1
chr2:169836427p.R692K1
chr2:169783678p.I1280I1
chr2:169869900p.R616H1

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 ABCB11 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 ABCB11

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

ABCB11,ADCY1,BCO2,ERICH3,C7,DEFB130,DHRS9,
GRB14,GSTA2,KIAA1377,LRP2,LRP4,NDST4,NPAS3,
NR5A1,PEX5L,PMCHL1,PMCHL2,SGCG,UBXN10,VRK2
ABCB11,ADH1A,ADH1B,ANKRD53,C6,CALCRL,CIDEA,
CNTFR,DNAH9,GHR,GLUL,HRSP12,IRAK2,NWD2,
LOC100190938,MOCS1,RGS17,RORB,SLC19A3,TM7SF2,AGMO

ABCB11,BTNL3,C11orf86,LINC00520,CA2,CEACAM7,CLCA4,
DHRS9,EDN3,EMP1,GDPD2,GDPD3,GUCA2B,MMP28,
MXD1,MYPN,OTOP2,PLAC8,SLC17A4,TMIGD1,TSPAN1
ABCB11,ANK3,AQP8,ARL15,LINC00597,CYP2B7P,EPB41L5,
FLNB,GLB1L2,HSPB3,LOC25845,ME3,PDE8A,PGAP3,
RUNDC1,SLC20A1,SLC45A2,SLC9A3,TAT,UNC5B,ZNF575
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 ABCB11
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB O95342; -.
ChemistryChEMBL CHEMBL6020; -.
Organism-specific databasesPharmGKB PA374; -.
Organism-specific databasesCTD 8647; -.

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 B (MDR/TAP), member 11approved; nutraceuticalAdenosine triphosphate
DB01016ATP-binding cassette, sub-family B (MDR/TAP), member 11approvedGlyburide
DB00143ATP-binding cassette, sub-family B (MDR/TAP), member 11approved; nutraceuticalGlutathione
DB00175ATP-binding cassette, sub-family B (MDR/TAP), member 11approvedPravastatin
DB00145ATP-binding cassette, sub-family B (MDR/TAP), member 11approved; nutraceuticalGlycine


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Cross referenced IDs for ABCB11
* 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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