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 SLCO1B1

Basic gene info.	Gene symbol	SLCO1B1
	Gene name	solute carrier organic anion transporter family, member 1B1
	Synonyms	HBLRR\|LST-1\|LST1\|OATP-C\|OATP1B1\|OATP2\|OATPC\|SLC21A6
	Cytomap	UCSC genome browser: 12p
	Genomic location	chr12 :21284127-21392730
	Type of gene	protein-coding
	RefGenes	NM_006446.4,
	Ensembl id	ENSG00000134538
	Description	OATP-2liver-specific organic anion transporter 1sodium-independent organic anion-transporting polypeptide 2solute carrier family 21 (organic anion transporter), member 6solute carrier family 21 member 6solute carrier organic anion transporter family
	Modification date	20141219
dbXrefs	MIM : 604843
	HGNC : HGNC
	Ensembl : ENSG00000134538
	HPRD : 09214
	Vega : OTTHUMG00000169047
Protein	UniProt: Q9Y6L6 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLCO1B1
	BioGPS: 10599
	Gene Expression Atlas: ENSG00000134538
	The Human Protein Atlas: ENSG00000134538
Pathway	NCI Pathway Interaction Database: SLCO1B1
	KEGG: SLCO1B1
	REACTOME: SLCO1B1
	ConsensusPathDB
	Pathway Commons: SLCO1B1
Metabolism	MetaCyc: SLCO1B1
	HUMANCyc: SLCO1B1
Regulation	Ensembl's Regulation: ENSG00000134538
	miRBase: chr12 :21,284,127-21,392,730
	TargetScan: NM_006446
	cisRED: ENSG00000134538
Context	iHOP: SLCO1B1
	cancer metabolism search in PubMed: SLCO1B1
	UCL Cancer Institute: SLCO1B1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SLCO1B1 in cancer cell metabolism	1. Lee E, Luo J, Su Y-C, Lewinger JP, Schumacher FR, et al. (2014) Hormone metabolism pathway genes and mammographic density change after quitting estrogen and progestin combined hormone therapy in the California Teachers Study. Breast Cancer Research 16: 477. go to article

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Phenotypic Information for SLCO1B1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SLCO1B1
	Familial Cancer Database: SLCO1B1

* 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	237450; phenotype. 604843; gene.
Orphanet	240851; Atorvastatin toxicity. 240903; Pravastatin toxicity. 240909; Rosuvastatin toxicity. 240913; Simvastatin toxicity. 240961; Susceptibility to adverse reaction due to atorvastatin treatment. 240981; Susceptibility to adverse reaction due to pravastatin treatment. 240983; Susceptibility to adverse reaction due to rosuvastatin treatment. 240985; Susceptibility to adverse reaction due to simvastatin treatment. 306566; Susceptibility to myopathies due to statin treatment. 3111; Rotor syndrome.
Disease	KEGG Disease: SLCO1B1
	MedGen: SLCO1B1 (Human Medical Genetics with Condition)
	ClinVar: SLCO1B1
Phenotype	MGI: SLCO1B1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SLCO1B1

Mutations for SLCO1B1

* 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	SLCO1B1	chr12	21307342	21307362	SOX5	chr12	23818452	23818472
pancreas	SLCO1B1	chr12	21311292	21311312	SLCO1B1	chr12	21312066	21312086
pancreas	SLCO1B1	chr12	21321987	21322007	SSPN	chr12	26368261	26368281

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 SLCO1B1 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

AI207430

EIF3A

372

120801566

120801937

SLCO1B1

362

658

21294366

21294662

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

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=121)	Stat. for Synonymous SNVs (# total SNVs=26)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=3)

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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
chr12:21353504-21353504	p.T345A	4
chr12:21329769-21329769	p.S140F	3
chr12:21327553-21327553	p.K90R	3
chr12:21375245-21375245	p.P565H	2
chr12:21331541-21331541	p.W171C	2
chr12:21329725-21329725	p.K125N	2
chr12:21329807-21329807	p.A153P	2
chr12:21329726-21329726	p.E126*	2
chr12:21358881-21358881	p.E471K	2
chr12:21370151-21370151	p.R532R	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=5

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	2		25			8		4			21	12	4		1	20	9		7
# mutation	6	2		20			8		4			23	12	4		1	22	11		13
nonsynonymous SNV	5	2		15			4		4			19	10	4		1	15	9		12
synonymous SNV	1			5			4					4	2				7	2		1

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
chr12:21353504	p.T345A	4
chr12:21349910	p.K160E	2
chr12:21370151	p.S272C	2
chr12:21325613	p.K160K	2
chr12:21377670	p.F38F	2
chr12:21331541	p.P588T	2
chr12:21349967	p.W171C	2
chr12:21377684	p.G592G	2
chr12:21329828	p.R532R	2
chr12:21325692	p.H451R	2

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 SLCO1B1 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 SLCO1B1

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


ACSM1,AKR1D1,ALOX15B,B3GAT1,C15orf43,LINC01554,C6orf223, FCN2,FKBP5,ISX,LST-3TM12,NANOG,RLN3,RNASE12, SERHL2,SERHL,SLC38A4,SLCO1B1,SPINK8,SPINT3,SULT1C3	ABCC11,ABCC2,AFMID,AKR1D1,AWAT2,B3GAT1,C6orf223, CHST1,CLDN14,GSTT2,HMGCR,HMGCS1,HPGD,LOC255167, MPV17L,MSMO1,SLC5A11,SLCO1B1,SYCP1,TARP,TMPRSS11F

ANGPTL3,BARHL2,C10orf120,C14orf184,CATSPERB,GPR27,HRG, IAPP,LIG1,TUSC7,LST-3TM12,MAMDC4,OR2AK2,PFKFB2, SLCO1B1,THEM4,TMEM19,TPD52L3,TRHR,VTN,ZFC3H1	ALB,APCS,C3P1,C8A,CFHR2,CFHR5,CYP4A22, DNAJB8,F13B,F9,FGG,ITIH2,KIR3DP1,KRTAP4-11, KRTAP5-3,LECT2,LOC100129935,LINC00160,OR1N1,SLC17A2,SLCO1B1

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 SLCO1B1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q9Y6L6; -.
Chemistry	ChEMBL	CHEMBL1697668; -.
Chemistry	GuidetoPHARMACOLOGY	1220; -.
Organism-specific databases	PharmGKB	PA134865839; -.
Organism-specific databases	CTD	10599; -.

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
DB01169	solute carrier organic anion transporter family, member 1B1	approved; investigational	Arsenic trioxide
DB00279	solute carrier organic anion transporter family, member 1B1	approved	Liothyronine
DB01053	solute carrier organic anion transporter family, member 1B1	approved	Penicillin G
DB00688	solute carrier organic anion transporter family, member 1B1	approved; investigational	Mycophenolate mofetil
DB00877	solute carrier organic anion transporter family, member 1B1	approved; investigational	Sirolimus
DB00683	solute carrier organic anion transporter family, member 1B1	illicit; approved	Midazolam
DB01016	solute carrier organic anion transporter family, member 1B1	approved	Glyburide
DB00257	solute carrier organic anion transporter family, member 1B1	approved	Clotrimazole
DB00834	solute carrier organic anion transporter family, member 1B1	approved; investigational	Mifepristone
DB01229	solute carrier organic anion transporter family, member 1B1	approved	Paclitaxel
DB00197	solute carrier organic anion transporter family, member 1B1	withdrawn	Troglitazone
DB00177	solute carrier organic anion transporter family, member 1B1	approved; investigational	Valsartan
DB00342	solute carrier organic anion transporter family, member 1B1	approved; withdrawn	Terfenadine
DB00520	solute carrier organic anion transporter family, member 1B1	approved	Caspofungin
DB00917	solute carrier organic anion transporter family, member 1B1	approved	Dinoprostone
DB01132	solute carrier organic anion transporter family, member 1B1	approved; investigational	Pioglitazone
DB00275	solute carrier organic anion transporter family, member 1B1	approved; investigational	Olmesartan
DB00563	solute carrier organic anion transporter family, member 1B1	approved	Methotrexate
DB00584	solute carrier organic anion transporter family, member 1B1	approved	Enalapril
DB00471	solute carrier organic anion transporter family, member 1B1	approved	Montelukast
DB00318	solute carrier organic anion transporter family, member 1B1	illicit; approved	Codeine
DB00295	solute carrier organic anion transporter family, member 1B1	approved; investigational	Morphine
DB00731	solute carrier organic anion transporter family, member 1B1	approved; investigational	Nateglinide
DB00412	solute carrier organic anion transporter family, member 1B1	approved; investigational	Rosiglitazone
DB00145	solute carrier organic anion transporter family, member 1B1	approved; nutraceutical	Glycine
DB00390	solute carrier organic anion transporter family, member 1B1	approved	Digoxin
DB01601	solute carrier organic anion transporter family, member 1B1	approved	Lopinavir
DB00641	solute carrier organic anion transporter family, member 1B1	approved	Simvastatin
DB01076	solute carrier organic anion transporter family, member 1B1	approved	Atorvastatin
DB00439	solute carrier organic anion transporter family, member 1B1	withdrawn	Cerivastatin
DB00343	solute carrier organic anion transporter family, member 1B1	approved	Diltiazem
DB01241	solute carrier organic anion transporter family, member 1B1	approved	Gemfibrozil
DB01167	solute carrier organic anion transporter family, member 1B1	approved; investigational	Itraconazole
DB00227	solute carrier organic anion transporter family, member 1B1	approved; investigational	Lovastatin
DB00503	solute carrier organic anion transporter family, member 1B1	approved; investigational	Ritonavir
DB00661	solute carrier organic anion transporter family, member 1B1	approved	Verapamil
DB00783	solute carrier organic anion transporter family, member 1B1	approved; investigational	Estradiol
DB00559	solute carrier organic anion transporter family, member 1B1	approved; investigational	Bosentan
DB00950	solute carrier organic anion transporter family, member 1B1	approved	Fexofenadine
DB00718	solute carrier organic anion transporter family, member 1B1	approved; investigational	Adefovir Dipivoxil
DB00501	solute carrier organic anion transporter family, member 1B1	approved	Cimetidine
DB00762	solute carrier organic anion transporter family, member 1B1	approved; investigational	Irinotecan
DB00912	solute carrier organic anion transporter family, member 1B1	approved; investigational	Repaglinide
DB01098	solute carrier organic anion transporter family, member 1B1	approved	Rosuvastatin
DB00973	solute carrier organic anion transporter family, member 1B1	approved	Ezetimibe
DB01045	solute carrier organic anion transporter family, member 1B1	approved	Rifampin
DB01095	solute carrier organic anion transporter family, member 1B1	approved	Fluvastatin
DB00175	solute carrier organic anion transporter family, member 1B1	approved	Pravastatin
DB00864	solute carrier organic anion transporter family, member 1B1	approved; investigational	Tacrolimus
DB01026	solute carrier organic anion transporter family, member 1B1	approved; investigational	Ketoconazole
DB01110	solute carrier organic anion transporter family, member 1B1	approved; investigational	Miconazole
DB00515	solute carrier organic anion transporter family, member 1B1	approved	Cisplatin

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Cross referenced IDs for SLCO1B1

* 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