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 SLCO1A2

Basic gene info.	Gene symbol	SLCO1A2
	Gene name	solute carrier organic anion transporter family, member 1A2
	Synonyms	OATP\|OATP-A\|OATP1A2\|SLC21A3
	Cytomap	UCSC genome browser: 12p12
	Genomic location	chr12 :21417533-21487832
	Type of gene	protein-coding
	RefGenes	NM_021094.3, NM_134431.3,NM_005075.2,
	Ensembl id	ENSG00000084453
	Description	OATP-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 date	20141207
dbXrefs	MIM : 602883
	HGNC : HGNC
	Ensembl : ENSG00000084453
	HPRD : 09112
	Vega : OTTHUMG00000156259
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLCO1A2
	BioGPS: 6579
	Gene Expression Atlas: ENSG00000084453
	The Human Protein Atlas: ENSG00000084453
Pathway	NCI Pathway Interaction Database: SLCO1A2
	KEGG: SLCO1A2
	REACTOME: SLCO1A2
	ConsensusPathDB
	Pathway Commons: SLCO1A2
Metabolism	MetaCyc: SLCO1A2
	HUMANCyc: SLCO1A2
Regulation	Ensembl's Regulation: ENSG00000084453
	miRBase: chr12 :21,417,533-21,487,832
	TargetScan: NM_021094
	cisRED: ENSG00000084453
Context	iHOP: SLCO1A2
	cancer metabolism search in PubMed: SLCO1A2
	UCL Cancer Institute: SLCO1A2
Assigned class in ccmGDB	C

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Phenotypic Information for SLCO1A2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: SLCO1A2
	MedGen: SLCO1A2 (Human Medical Genetics with Condition)
	ClinVar: SLCO1A2
Phenotype	MGI: SLCO1A2 (International Mouse Phenotyping Consortium)
Phenotype	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.

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	SLCO1A2	chr12	21455831	21455851	ITGB3	chr17	45380547	45380567
pancreas	SLCO1A2	chr12	21456957	21456977	GOLT1B	chr12	21655902	21655922
pancreas	SLCO1A2	chr12	21457878	21457898	ITGB3	chr17	45380752	45380772
pancreas	SLCO1A2	chr12	21465712	21465732	SLCO1A2	chr12	21465455	21465475

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 SLCO1A2 related fusion information.

ID	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
BP387918	SLCO1A2	1	65	12	21531697	21531761	HP1BP3	61	318	1	21069661	21069918
BP386860	SLCO1A2	1	240	12	21532366	21532605	PPY	241	530	17	42018174	42018901
CA866148	LIN7C	6	347	11	27516433	27516774	SLCO1A2	344	401	12	21531224	21531281
BP384906	SH3BP5	1	80	3	15368962	15369040	SLCO1A2	71	494	12	21531983	21532405
BQ786844	PSTK	14	259	10	124745251	124745496	SLCO1A2	257	528	12	21531462	21531733

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=4

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Somatic 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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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
chr12:21457496-21457496	p.E152K	4
chr12:21457408-21457408	p.S181F	4
chr12:21453303-21453303	p.E297K	3
chr12:21422536-21422536	p.D653D	2
chr12:21445246-21445246	p.Q488E	2
chr12:21422553-21422553	p.E648K	2
chr12:21453469-21453469	p.W241C	2
chr12:21471819-21471819	p.K33K	2
chr12:21467552-21467552	p.I89T	2
chr12:21446932-21446932	p.L462L	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=4

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	2	2		7	1		5		4			12	6	1			27	3	1	10
# mutation	2	2		9	1		5		4			12	6	1			26	3	1	12
nonsynonymous SNV	1	1		7	1		3		1			9	5	1			17	3	1	8
synonymous SNV	1	1		2			2		3			3	1				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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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
chr12:21457408	p.S181F,SLCO1A2	4
chr12:21453303	p.E297K,SLCO1A2	3
chr12:21446932	p.E648K,SLCO1A2	2
chr12:21422553	p.L462L,SLCO1A2	2
chr12:21446942	p.L23V,SLCO1A2	1
chr12:21457417	p.L666L,SLCO1A2	1
chr12:21422638	p.S517P,SLCO1A2	1
chr12:21450479	p.I336I,SLCO1A2	1
chr12:21459842	p.P236T,SLCO1A2	1
chr12:21471799	p.E152K,SLCO1A2	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 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

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


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

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 SLCO1A2

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
DB00286	solute carrier organic anion transporter family, member 1A2	approved	Conjugated Estrogens
DB00563	solute carrier organic anion transporter family, member 1A2	approved	Methotrexate
DB00537	solute carrier organic anion transporter family, member 1A2	approved; investigational	Ciprofloxacin
DB00467	solute carrier organic anion transporter family, member 1A2	approved	Enoxacin
DB01044	solute carrier organic anion transporter family, member 1A2	approved; investigational	Gatifloxacin
DB01137	solute carrier organic anion transporter family, member 1A2	approved; investigational	Levofloxacin
DB00279	solute carrier organic anion transporter family, member 1A2	approved	Liothyronine
DB00978	solute carrier organic anion transporter family, member 1A2	approved	Lomefloxacin
DB01059	solute carrier organic anion transporter family, member 1A2	approved	Norfloxacin
DB00728	solute carrier organic anion transporter family, member 1A2	approved	Rocuronium
DB01098	solute carrier organic anion transporter family, member 1A2	approved	Rosuvastatin
DB01232	solute carrier organic anion transporter family, member 1A2	approved; investigational	Saquinavir
DB00619	solute carrier organic anion transporter family, member 1A2	approved	Imatinib
DB01092	solute carrier organic anion transporter family, member 1A2	approved	Ouabain
DB00175	solute carrier organic anion transporter family, member 1A2	approved	Pravastatin
DB00199	solute carrier organic anion transporter family, member 1A2	approved	Erythromycin
DB00145	solute carrier organic anion transporter family, member 1A2	approved; nutraceutical	Glycine
DB01601	solute carrier organic anion transporter family, member 1A2	approved	Lopinavir
DB00950	solute carrier organic anion transporter family, member 1A2	approved	Fexofenadine
DB00564	solute carrier organic anion transporter family, member 1A2	approved; investigational	Carbamazepine

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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