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 SLCO1A2
Basic gene info.Gene symbolSLCO1A2
Gene namesolute carrier organic anion transporter family, member 1A2
SynonymsOATP|OATP-A|OATP1A2|SLC21A3
CytomapUCSC genome browser: 12p12
Genomic locationchr12 :21417533-21487832
Type of geneprotein-coding
RefGenesNM_021094.3,
NM_134431.3,NM_005075.2,
Ensembl idENSG00000084453
DescriptionOATP-1organic anion transporting polypeptide Aorganic anion-transporting polypeptide 1sodium-independent organic anion transportersolute carrier family 21 (organic anion transporter), member 3solute carrier family 21 member 3solute carrier organic a
Modification date20141207
dbXrefs MIM : 602883
HGNC : HGNC
Ensembl : ENSG00000084453
HPRD : 09112
Vega : OTTHUMG00000156259
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLCO1A2
BioGPS: 6579
Gene Expression Atlas: ENSG00000084453
The Human Protein Atlas: ENSG00000084453
PathwayNCI Pathway Interaction Database: SLCO1A2
KEGG: SLCO1A2
REACTOME: SLCO1A2
ConsensusPathDB
Pathway Commons: SLCO1A2
MetabolismMetaCyc: SLCO1A2
HUMANCyc: SLCO1A2
RegulationEnsembl's Regulation: ENSG00000084453
miRBase: chr12 :21,417,533-21,487,832
TargetScan: NM_021094
cisRED: ENSG00000084453
ContextiHOP: SLCO1A2
cancer metabolism search in PubMed: SLCO1A2
UCL Cancer Institute: SLCO1A2
Assigned class in ccmGDBC

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Phenotypic Information for SLCO1A2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLCO1A2
Familial Cancer Database: SLCO1A2
* 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: SLCO1A2
MedGen: SLCO1A2 (Human Medical Genetics with Condition)
ClinVar: SLCO1A2
PhenotypeMGI: SLCO1A2 (International Mouse Phenotyping Consortium)
PhenomicDB: SLCO1A2

Mutations for SLCO1A2
* 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
pancreasSLCO1A2chr122145583121455851ITGB3chr174538054745380567
pancreasSLCO1A2chr122145695721456977GOLT1Bchr122165590221655922
pancreasSLCO1A2chr122145787821457898ITGB3chr174538075245380772
pancreasSLCO1A2chr122146571221465732SLCO1A2chr122146545521465475
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 SLCO1A2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP387918SLCO1A2165122153169721531761HP1BP36131812106966121069918
BP386860SLCO1A21240122153236621532605PPY241530174201817442018901
CA866148LIN7C6347112751643327516774SLCO1A2344401122153122421531281
BP384906SH3BP518031536896215369040SLCO1A271494122153198321532405
BQ786844PSTK1425910124745251124745496SLCO1A2257528122153146221531733

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 # sample11    1   1      
GAIN (# sample)11    1   1      
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=62)
Stat. for Synonymous SNVs
(# total SNVs=23)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr12:21457496-21457496p.E152K4
chr12:21457408-21457408p.S181F4
chr12:21453303-21453303p.E297K3
chr12:21446932-21446932p.L462L2
chr12:21459834-21459834p.P142A2
chr12:21487532-21487532p.S17F2
chr12:21422520-21422520p.T659A2
chr12:21422680-21422680p.P605P2
chr12:21445246-21445246p.Q488E2
chr12:21422536-21422536p.D653D2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22 71 5 4  1261  273110
# mutation22 91 5 4  1261  263112
nonsynonymous SNV11 71 3 1  951  17318
synonymous SNV11 2  2 3  31   9  4
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
chr12:21457408p.S181F,SLCO1A24
chr12:21453303p.E297K,SLCO1A23
chr12:21446932p.E648K,SLCO1A22
chr12:21422553p.L462L,SLCO1A22
chr12:21450370p.G348E,SLCO1A21
chr12:21457474p.A244T,SLCO1A21
chr12:21453315p.V159E,SLCO1A21
chr12:21471722p.M40T,SLCO1A21
chr12:21427475p.S525Y,SLCO1A21
chr12:21457393p.P340S,SLCO1A21

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 SLCO1A2 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 SLCO1A2

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

AIMP1,AMBN,C17orf78,C8orf74,CCDC34,IAPP,KCNJ16,
LDHB,LEPREL1,LOC100302401,MEST,MESTIT1,MOB3B,NCALD,
NECAB2,OR3A3,PROL1,RNLS,SLCO1A2,UGT1A8,WNT8B
ATL2,B3GALT5,DIEXF,B3GALT5-AS1,CHST9,ELF5,GPCPD1,
IGSF5,ITGA6,LARS,LOC284578,LOC286467,LPPR1,NALCN,
SLC5A1,SLCO1A2,SNHG1,SNHG4,SPHKAP,TAF4B,TMEM87A

BIRC8,LINC01551,CFC1B,CNPY1,CPNE4,FAM47C,FNDC7,
GPR98,KCNQ2,KREMEN2,MPPED1,NLRP4,RD3,SERPINA5,
SLCO1A2,SPOCK3,SPSB4,ST8SIA5,TEKT2,TMEM145,USH1G
AMTN,ANKRD55,LRIF1,C4orf45,CHIA,PRR32,DUSP13,
GAGE12J,HAVCR1,IL7R,KRT34,KRTAP4-7,LCE1F,LCE4A,
MAGEA2,SCN10A,SERPINB13,SLCO1A2,SSX1,SSX2,TMPRSS11A,
UG
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 SLCO1A2
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
DB00286solute carrier organic anion transporter family, member 1A2approvedConjugated Estrogens
DB00563solute carrier organic anion transporter family, member 1A2approvedMethotrexate
DB00537solute carrier organic anion transporter family, member 1A2approved; investigationalCiprofloxacin
DB00467solute carrier organic anion transporter family, member 1A2approvedEnoxacin
DB01044solute carrier organic anion transporter family, member 1A2approved; investigationalGatifloxacin
DB01137solute carrier organic anion transporter family, member 1A2approved; investigationalLevofloxacin
DB00279solute carrier organic anion transporter family, member 1A2approvedLiothyronine
DB00978solute carrier organic anion transporter family, member 1A2approvedLomefloxacin
DB01059solute carrier organic anion transporter family, member 1A2approvedNorfloxacin
DB00728solute carrier organic anion transporter family, member 1A2approvedRocuronium
DB01098solute carrier organic anion transporter family, member 1A2approvedRosuvastatin
DB01232solute carrier organic anion transporter family, member 1A2approved; investigationalSaquinavir
DB00619solute carrier organic anion transporter family, member 1A2approvedImatinib
DB01092solute carrier organic anion transporter family, member 1A2approvedOuabain
DB00175solute carrier organic anion transporter family, member 1A2approvedPravastatin
DB00199solute carrier organic anion transporter family, member 1A2approvedErythromycin
DB00145solute carrier organic anion transporter family, member 1A2approved; nutraceuticalGlycine
DB01601solute carrier organic anion transporter family, member 1A2approvedLopinavir
DB00950solute carrier organic anion transporter family, member 1A2approvedFexofenadine
DB00564solute carrier organic anion transporter family, member 1A2approved; investigationalCarbamazepine


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Cross referenced IDs for SLCO1A2
* 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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