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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
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. |
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Oncogene 1 | Significant driver gene in |
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 |
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 | Top |
- 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 |
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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 | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 1 | 1 |   |   |   |   | 1 |   |   |   | 1 |   |   |   |   |   |   | |||
GAIN (# sample) | 1 | 1 |   |   |   |   | 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=62) | (# total SNVs=23) |
(# total SNVs=1) | (# 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 |
chr12:21446932-21446932 | p.L462L | 2 |
chr12:21459834-21459834 | p.P142A | 2 |
chr12:21487532-21487532 | p.S17F | 2 |
chr12:21422520-21422520 | p.T659A | 2 |
chr12:21422680-21422680 | p.P605P | 2 |
chr12:21422536-21422536 | p.D653D | 2 |
chr12:21445246-21445246 | p.Q488E | 2 |
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SNV Counts per Each Loci in TCGA data |
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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 |
chr12:21448710 | p.P562P,SLCO1A2 | 1 |
chr12:21457448 | p.M377I,SLCO1A2 | 1 |
chr12:21427408 | p.E292K,SLCO1A2 | 1 |
chr12:21453304 | p.P174P,SLCO1A2 | 1 |
chr12:21467564 | p.S64I,SLCO1A2 | 1 |
chr12:21445246 | p.T555R,SLCO1A2 | 1 |
Other DBs for Point Mutations |
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. |
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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 |
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 |
* 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 |
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Interacting Genes (from Pathway Commons) |
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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 |
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