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 SLCO1B3

Basic gene info.	Gene symbol	SLCO1B3
	Gene name	solute carrier organic anion transporter family, member 1B3
	Synonyms	HBLRR\|LST-2\|LST-3TM13\|LST3\|OATP-8\|OATP1B3\|OATP8\|SLC21A8
	Cytomap	UCSC genome browser: 12p12
	Genomic location	chr12 :20963637-21069843
	Type of gene	protein-coding
	RefGenes	NM_019844.3,
	Ensembl id	ENSG00000111700
	Description	liver-specific organic anion transporter 2liver-specific organic anion transporter 3TM13organic anion transporter 8organic anion transporter LST-3corganic anion-transporting polypeptide 8solute carrier family 21 (organic anion transporter), member 8
	Modification date	20141219
dbXrefs	MIM : 605495
	HGNC : HGNC
	Ensembl : ENSG00000111700
	HPRD : 12021
	Vega : OTTHUMG00000169011
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLCO1B3
	BioGPS: 28234
	Gene Expression Atlas: ENSG00000111700
	The Human Protein Atlas: ENSG00000111700
Pathway	NCI Pathway Interaction Database: SLCO1B3
	KEGG: SLCO1B3
	REACTOME: SLCO1B3
	ConsensusPathDB
	Pathway Commons: SLCO1B3
Metabolism	MetaCyc: SLCO1B3
	HUMANCyc: SLCO1B3
Regulation	Ensembl's Regulation: ENSG00000111700
	miRBase: chr12 :20,963,637-21,069,843
	TargetScan: NM_019844
	cisRED: ENSG00000111700
Context	iHOP: SLCO1B3
	cancer metabolism search in PubMed: SLCO1B3
	UCL Cancer Institute: SLCO1B3
Assigned class in ccmGDB	C

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Phenotypic Information for SLCO1B3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SLCO1B3
	Familial Cancer Database: SLCO1B3

* 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
Orphanet
Disease	KEGG Disease: SLCO1B3
	MedGen: SLCO1B3 (Human Medical Genetics with Condition)
	ClinVar: SLCO1B3
Phenotype	MGI: SLCO1B3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SLCO1B3

Mutations for SLCO1B3

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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	SLCO1B3	chr12	21052667	21052667	CASC1	chr12	25297321	25297321
pancreas	SLCO1B3	chr12	21061863	21061883	SLCO1B3	chr12	21066243	21066263

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 SLCO1B3 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

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=7

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=95)	Stat. for Synonymous SNVs (# total SNVs=28)

Stat. for Deletions (# total SNVs=5)	Stat. for Insertions (# total SNVs=5)

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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
chr12:21011428-21011428	p.P94P	6
chr12:21032513-21032513	p.P427S	3
chr12:21033868-21033868	p.E471K	3
chr12:21069011-21069011	p.M647V	3
chr12:21032524-21032524	p.C430C	3
chr12:21032525-21032525	p.E431K	3
chr12:21036398-21036398	p.R515K	3
chr12:21054322-21054322	p.D596H	3
chr12:21032478-21032478	p.S415L	3
chr12:21036450-21036450	p.R532R	3

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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=6

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	4	6		17	1		7		5	1		15	9	2	1		40	8		9
# mutation	4	6		14	1		7		5	1		15	11	2	1		48	9		11
nonsynonymous SNV	4	5		12	1		5		3	1		10	6		1		36	9		8
synonymous SNV		1		2			2		2			5	5	2			12			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])

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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
chr12:21011428	p.P94P	5
chr12:21054322	p.D596H	3
chr12:21036398	p.R532R	3
chr12:21032478	p.S415L	3
chr12:21036450	p.R515K	3
chr12:21051426	p.I380I	2
chr12:21028196	p.E471K	2
chr12:21036503	p.S618S	2
chr12:21028199	p.S252Y	2
chr12:21069011	p.T550I	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 SLCO1B3 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 SLCO1B3

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


BHMT,CALB1,CCL24,CDA,CSF2,DEFB103B,GGT8P, IFNK,IL1A,KCNV1,KRT6A,KRTAP11-1,LAMC2,LANCL3, LOC285045,LY75,REG1A,RNASE10,SLCO1B3,TRIML2,WNT7A	BAAT,CDH17,CDHR2,FAM9A,FBXW10,FOXR2,GKN2, GPR52,KRTAP13-1,KRTAP27-1,NAPSA,OR13C8,OR6X1,PLA2G10, PSAPL1,SCGB3A2,SFTA3,SFTPB,SLCO1B3,TM4SF20,TM4SF5

ANXA2P2,CCDC109B,CXCL11,GLRX3,JAG1,LRRC40,LST-3TM12, LYPD1,MMP7,NRADDP,OR4F15,PSMA6,PSMD8,PSME1, SERPINB5,SLCO1B1,SLCO1B3,SNX6,TXNL1,USP15,WDR41	ACTL7A,ANGPTL3,C12orf71,C6orf141,CLDN17,ELFN1,GLIS3, IL11,LRRC8B,MAT2A,NPHP3-AS1,NLRP10,NOS3,PRRX2, PVR,SLCO1B3,TACSTD2,TC2N,TPBG,TRIM16,TSGA13

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 SLCO1B3

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB00390	solute carrier organic anion transporter family, member 1B3	approved	Digoxin
DB00584	solute carrier organic anion transporter family, member 1B3	approved	Enalapril
DB00279	solute carrier organic anion transporter family, member 1B3	approved	Liothyronine
DB00563	solute carrier organic anion transporter family, member 1B3	approved	Methotrexate
DB00275	solute carrier organic anion transporter family, member 1B3	approved; investigational	Olmesartan
DB01092	solute carrier organic anion transporter family, member 1B3	approved	Ouabain
DB00966	solute carrier organic anion transporter family, member 1B3	approved; investigational	Telmisartan
DB00177	solute carrier organic anion transporter family, member 1B3	approved; investigational	Valsartan
DB00688	solute carrier organic anion transporter family, member 1B3	approved; investigational	Mycophenolate mofetil
DB00877	solute carrier organic anion transporter family, member 1B3	approved; investigational	Sirolimus
DB00864	solute carrier organic anion transporter family, member 1B3	approved; investigational	Tacrolimus
DB00199	solute carrier organic anion transporter family, member 1B3	approved	Erythromycin
DB01241	solute carrier organic anion transporter family, member 1B3	approved	Gemfibrozil
DB00145	solute carrier organic anion transporter family, member 1B3	approved; nutraceutical	Glycine
DB01095	solute carrier organic anion transporter family, member 1B3	approved	Fluvastatin
DB01098	solute carrier organic anion transporter family, member 1B3	approved	Rosuvastatin
DB01601	solute carrier organic anion transporter family, member 1B3	approved	Lopinavir
DB01229	solute carrier organic anion transporter family, member 1B3	approved	Paclitaxel
DB00559	solute carrier organic anion transporter family, member 1B3	approved; investigational	Bosentan
DB01045	solute carrier organic anion transporter family, member 1B3	approved	Rifampin
DB00950	solute carrier organic anion transporter family, member 1B3	approved	Fexofenadine
DB00718	solute carrier organic anion transporter family, member 1B3	approved; investigational	Adefovir Dipivoxil
DB00501	solute carrier organic anion transporter family, member 1B3	approved	Cimetidine
DB01248	solute carrier organic anion transporter family, member 1B3	approved; investigational	Docetaxel
DB00973	solute carrier organic anion transporter family, member 1B3	approved	Ezetimibe
DB01024	solute carrier organic anion transporter family, member 1B3	approved	Mycophenolic acid
DB00762	solute carrier organic anion transporter family, member 1B3	approved; investigational	Irinotecan

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Cross referenced IDs for SLCO1B3

* 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