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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SLC22A2 |
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Phenotypic Information for SLC22A2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SLC22A2 |
Familial Cancer Database: SLC22A2 |
* This gene is included in those cancer gene databases. |
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_ABACAVIR_TRANSPORT_AND_METABOLISM |
Mutations for SLC22A2 |
* 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 |
There's no inter-chromosomal structural variation. |
- 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 | SLC22A2 | chr6 | 160641959 | 160641979 | chr6 | 119680562 | 119680582 |
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 SLC22A2 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 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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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=54) | (# total SNVs=32) |
(# total SNVs=2) | (# total SNVs=0) |
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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 |
chr6:160671634-160671634 | p.R207C | 4 |
chr6:160679569-160679569 | p.T74M | 3 |
chr6:160662608-160662608 | p.V467I | 3 |
chr6:160679775-160679775 | p.V5V | 3 |
chr6:160664724-160664724 | p.E387K | 2 |
chr6:160679772-160679772 | p.D6D | 2 |
chr6:160668235-160668235 | p.S313Y | 2 |
chr6:160679619-160679619 | p.A57A | 2 |
chr6:160679400-160679400 | p.T130T | 2 |
chr6:160679514-160679514 | p.Y92Y | 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 | 1 | 1 |   | 5 | 4 |   | 4 |   | 1 | 1 |   | 9 | 6 | 1 |   |   | 19 | 6 | 1 | 14 |
# mutation | 1 | 1 |   | 5 | 4 |   | 4 |   | 1 | 1 |   | 9 | 6 | 1 |   |   | 22 | 6 | 1 | 20 |
nonsynonymous SNV |   | 1 |   | 4 | 3 |   | 3 |   | 1 | 1 |   | 3 | 4 | 1 |   |   | 13 | 4 |   | 6 |
synonymous SNV | 1 |   |   | 1 | 1 |   | 1 |   |   |   |   | 6 | 2 |   |   |   | 9 | 2 | 1 | 14 |
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 |
chr6:160679775 | p.V5V | 3 |
chr6:160679514 | p.Y92Y | 2 |
chr6:160664675 | p.R403H | 2 |
chr6:160679619 | p.A57A | 2 |
chr6:160679627 | p.R231Q | 1 |
chr6:160662519 | p.D124D | 1 |
chr6:160670319 | p.F33F | 1 |
chr6:160664693 | p.G477V | 1 |
chr6:160677683 | p.T348T | 1 |
chr6:160679479 | p.E227K | 1 |
Other DBs for Point Mutations |
Copy Number for SLC22A2 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 SLC22A2 |
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 |
CALCA,CRLF1,CRTAC1,CYSLTR2,FILIP1,GPR133,GUCY2GP, IL15,IRF4,LOC154822,MAPK4,PDE3A,PLA2G2A,PLA2G4A, PPARGC1A,SLAIN1,SLC22A2,SLC22A3,USH1C,VAT1L,WNT1 | VRTN,C1QTNF8,C7orf33,CLPS,COL9A1,CPNE6,DKFZP434H168, DRP2,HBG2,HTR1B,ITIH3,ITLN1,KIF1A,MLC1, NKX2-3,NOBOX,P2RX1,SLC22A2,SOST,WFDC1,ZFP42 | ||||
AIPL1,CARD17,CLIC2,CT62,CXorf30,ENHO,FAM131B, FAM178B,IL12RB1,ILDR2,KCNC4,LOC645431,MYH6,OR52N2, OR7C2,PSG10P,RAB9B,RAET1E,RBP4,SLC22A2,TAS2R7 | C20orf166-AS1,C9orf9,CC2D2A,CTF1,DPP6,ESYT3,FAM129A, FBXL22,FXYD6,COLGALT2,KANK2,KLHDC8B,MAB21L2,MAP6, NPHP1,NPTX1,SLC22A2,STAC,TCEAL2,TUBG2,WDR17 |
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 SLC22A2 |
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 |
DB00331 | solute carrier family 22 (organic cation transporter), member 2 | approved | Metformin | ||
DB00690 | solute carrier family 22 (organic cation transporter), member 2 | illicit; approved | Flurazepam | ||
DB00988 | solute carrier family 22 (organic cation transporter), member 2 | approved | Dopamine | ||
DB00126 | solute carrier family 22 (organic cation transporter), member 2 | approved; nutraceutical | Vitamin C | ||
DB00122 | solute carrier family 22 (organic cation transporter), member 2 | approved; nutraceutical | Choline | ||
DB00501 | solute carrier family 22 (organic cation transporter), member 2 | approved | Cimetidine | ||
DB00958 | solute carrier family 22 (organic cation transporter), member 2 | approved | Carboplatin | ||
DB00515 | solute carrier family 22 (organic cation transporter), member 2 | approved | Cisplatin | ||
DB00526 | solute carrier family 22 (organic cation transporter), member 2 | approved; investigational | Oxaliplatin | ||
DB01273 | solute carrier family 22 (organic cation transporter), member 2 | approved; investigational | Varenicline | ||
DB00879 | solute carrier family 22 (organic cation transporter), member 2 | approved; investigational | Emtricitabine | ||
DB00709 | solute carrier family 22 (organic cation transporter), member 2 | approved; investigational | Lamivudine | ||
DB00495 | solute carrier family 22 (organic cation transporter), member 2 | approved | Zidovudine |
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Cross referenced IDs for SLC22A2 |
* 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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