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 SLCO1B3
Basic gene info.Gene symbolSLCO1B3
Gene namesolute carrier organic anion transporter family, member 1B3
SynonymsHBLRR|LST-2|LST-3TM13|LST3|OATP-8|OATP1B3|OATP8|SLC21A8
CytomapUCSC genome browser: 12p12
Genomic locationchr12 :20963637-21069843
Type of geneprotein-coding
RefGenesNM_019844.3,
Ensembl idENSG00000111700
Descriptionliver-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 date20141219
dbXrefs MIM : 605495
HGNC : HGNC
Ensembl : ENSG00000111700
HPRD : 12021
Vega : OTTHUMG00000169011
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLCO1B3
BioGPS: 28234
Gene Expression Atlas: ENSG00000111700
The Human Protein Atlas: ENSG00000111700
PathwayNCI Pathway Interaction Database: SLCO1B3
KEGG: SLCO1B3
REACTOME: SLCO1B3
ConsensusPathDB
Pathway Commons: SLCO1B3
MetabolismMetaCyc: SLCO1B3
HUMANCyc: SLCO1B3
RegulationEnsembl's Regulation: ENSG00000111700
miRBase: chr12 :20,963,637-21,069,843
TargetScan: NM_019844
cisRED: ENSG00000111700
ContextiHOP: SLCO1B3
cancer metabolism search in PubMed: SLCO1B3
UCL Cancer Institute: SLCO1B3
Assigned class in ccmGDBC

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Phenotypic Information for SLCO1B3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SLCO1B3
MedGen: SLCO1B3 (Human Medical Genetics with Condition)
ClinVar: SLCO1B3
PhenotypeMGI: SLCO1B3 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasSLCO1B3chr122105266721052667CASC1chr122529732125297321
pancreasSLCO1B3chr122106186321061883SLCO1B3chr122106624321066263
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 SLCO1B3 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 # sample1    1  2 1   2  
GAIN (# sample)1    1  2 1   2  
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=7

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check002.gifSomatic 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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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
chr12:21011428-21011428p.P94P6
chr12:21032513-21032513p.P427S3
chr12:21069011-21069011p.M647V3
chr12:21033868-21033868p.E471K3
chr12:21032524-21032524p.C430C3
chr12:21032525-21032525p.E431K3
chr12:21054322-21054322p.D596H3
chr12:21036398-21036398p.R515K3
chr12:21032478-21032478p.S415L3
chr12:21036450-21036450p.R532R3

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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=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample46 171 7 51 15921 408 9
# mutation46 141 7 51 151121 489 11
nonsynonymous SNV45 121 5 31 106 1 369 8
synonymous SNV 1 2  2 2  552  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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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
chr12:21011428p.P94P5
chr12:21054322p.D596H3
chr12:21036398p.R532R3
chr12:21032478p.S415L3
chr12:21036450p.R515K3
chr12:21051426p.I380I2
chr12:21028196p.S618S2
chr12:21028199p.E471K2
chr12:21036503p.S252Y2
chr12:21069011p.R253P2

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 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

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

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
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 SLCO1B3
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
DB00390solute carrier organic anion transporter family, member 1B3approvedDigoxin
DB00584solute carrier organic anion transporter family, member 1B3approvedEnalapril
DB00279solute carrier organic anion transporter family, member 1B3approvedLiothyronine
DB00563solute carrier organic anion transporter family, member 1B3approvedMethotrexate
DB00275solute carrier organic anion transporter family, member 1B3approved; investigationalOlmesartan
DB01092solute carrier organic anion transporter family, member 1B3approvedOuabain
DB00966solute carrier organic anion transporter family, member 1B3approved; investigationalTelmisartan
DB00177solute carrier organic anion transporter family, member 1B3approved; investigationalValsartan
DB00688solute carrier organic anion transporter family, member 1B3approved; investigationalMycophenolate mofetil
DB00877solute carrier organic anion transporter family, member 1B3approved; investigationalSirolimus
DB00864solute carrier organic anion transporter family, member 1B3approved; investigationalTacrolimus
DB00199solute carrier organic anion transporter family, member 1B3approvedErythromycin
DB01241solute carrier organic anion transporter family, member 1B3approvedGemfibrozil
DB00145solute carrier organic anion transporter family, member 1B3approved; nutraceuticalGlycine
DB01095solute carrier organic anion transporter family, member 1B3approvedFluvastatin
DB01098solute carrier organic anion transporter family, member 1B3approvedRosuvastatin
DB01601solute carrier organic anion transporter family, member 1B3approvedLopinavir
DB01229solute carrier organic anion transporter family, member 1B3approvedPaclitaxel
DB00559solute carrier organic anion transporter family, member 1B3approved; investigationalBosentan
DB01045solute carrier organic anion transporter family, member 1B3approvedRifampin
DB00950solute carrier organic anion transporter family, member 1B3approvedFexofenadine
DB00718solute carrier organic anion transporter family, member 1B3approved; investigationalAdefovir Dipivoxil
DB00501solute carrier organic anion transporter family, member 1B3approvedCimetidine
DB01248solute carrier organic anion transporter family, member 1B3approved; investigationalDocetaxel
DB00973solute carrier organic anion transporter family, member 1B3approvedEzetimibe
DB01024solute carrier organic anion transporter family, member 1B3approvedMycophenolic acid
DB00762solute carrier organic anion transporter family, member 1B3approved; investigationalIrinotecan


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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



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