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 ABCB11

Basic gene info.	Gene symbol	ABCB11
	Gene name	ATP-binding cassette, sub-family B (MDR/TAP), member 11
	Synonyms	ABC16\|BRIC2\|BSEP\|PFIC-2\|PFIC2\|PGY4\|SPGP
	Cytomap	UCSC genome browser: 2q24
	Genomic location	chr2 :169779448-169887833
	Type of gene	protein-coding
	RefGenes	NM_003742.2,
	Ensembl id	ENSG00000263298
	Description	ABC member 16, MDR/TAP subfamilyATP-binding cassette sub-family B member 11bile salt export pumpprogressive familial intrahepatic cholestasis 2sister p-glycoprotein
	Modification date	20141207
dbXrefs	MIM : 603201
	HGNC : HGNC
	Ensembl : ENSG00000073734
	HPRD : 04436
	Vega : OTTHUMG00000154039
Protein	UniProt: O95342 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ABCB11
	BioGPS: 8647
	Gene Expression Atlas: ENSG00000263298
	The Human Protein Atlas: ENSG00000263298
Pathway	NCI Pathway Interaction Database: ABCB11
	KEGG: ABCB11
	REACTOME: ABCB11
	ConsensusPathDB
	Pathway Commons: ABCB11
Metabolism	MetaCyc: ABCB11
	HUMANCyc: ABCB11
Regulation	Ensembl's Regulation: ENSG00000263298
	miRBase: chr2 :169,779,448-169,887,833
	TargetScan: NM_003742
	cisRED: ENSG00000263298
Context	iHOP: ABCB11
	cancer metabolism search in PubMed: ABCB11
	UCL Cancer Institute: ABCB11
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ABCB11 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
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.
Disease	KEGG Disease: ABCB11
	MedGen: ABCB11 (Human Medical Genetics with Condition)
	ClinVar: ABCB11
Phenotype	MGI: ABCB11 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	ABCB11	chr2	169800247	169800267	NOSTRIN	chr2	169719372	169719392

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 ABCB11 related fusion information.

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

AA984265

SRP14

141

40331085

40331369

ABCB11

142

458

169869119

169869435

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	6	1		1					5		4		3				5
GAIN (# sample)	2	1							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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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=4

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Somatic 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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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
chr2:169780250-169780250	p.A1283V	4
chr2:169814479-169814479	p.L780I	4
chr2:169828491-169828491	p.E502Q	2
chr2:169847412-169847412	p.Y269Y	2
chr2:169781166-169781166	p.?	2
chr2:169842673-169842673	p.G344S	2
chr2:169787307-169787307	p.S1093S	2
chr2:169783815-169783815	p.G1157R	2
chr2:169851889-169851889	p.S194*	2
chr2:169869891-169869891	p.D94H	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=2

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		22	4		7		3		1	24	7	2			33	11	1	15
# mutation		6		27	4		9		3		1	27	7	2			47	13	1	20
nonsynonymous SNV		5		20	2		6		3		1	18	6	2			33	10	1	15
synonymous SNV		1		7	2		3					9	1				14	3		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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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
chr2:169814479	p.D94N	2
chr2:169842636	p.Q1215H	2
chr2:169842673	p.G1267S	2
chr2:169780299	p.P356Q	2
chr2:169781287	p.G344S	2
chr2:169869891	p.L780V	2
chr2:169824975	p.I891I	1
chr2:169836427	p.R692K	1
chr2:169783678	p.I1280I	1
chr2:169869900	p.R616H	1

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 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

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


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

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 ABCB11

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	O95342; -.
Chemistry	ChEMBL	CHEMBL6020; -.
Organism-specific databases	PharmGKB	PA374; -.
Organism-specific databases	CTD	8647; -.

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 B (MDR/TAP), member 11	approved; nutraceutical	Adenosine triphosphate
DB01016	ATP-binding cassette, sub-family B (MDR/TAP), member 11	approved	Glyburide
DB00143	ATP-binding cassette, sub-family B (MDR/TAP), member 11	approved; nutraceutical	Glutathione
DB00175	ATP-binding cassette, sub-family B (MDR/TAP), member 11	approved	Pravastatin
DB00145	ATP-binding cassette, sub-family B (MDR/TAP), member 11	approved; nutraceutical	Glycine

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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