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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SLC22A1 |
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Phenotypic Information for SLC22A1(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: SLC22A1 |
Familial Cancer Database: SLC22A1 |
* 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/ |
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REACTOME_ABACAVIR_TRANSPORT_AND_METABOLISM |
Mutations for SLC22A1 |
* 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SLC22A1 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 |
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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 |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |
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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Stat. for Non-Synonymous SNVs (# total SNVs=52) | (# total SNVs=14) |
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(# total SNVs=0) | (# total SNVs=1) |
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* 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 |
chr6:160560898-160560905 | p.? | 11 |
chr6:160560884-160560884 | p.I421F | 3 |
chr6:160543123-160543123 | p.S52S | 3 |
chr6:160557328-160557328 | p.A306T | 2 |
chr6:160543066-160543066 | p.A33A | 2 |
chr6:160555087-160555087 | p.A257T | 2 |
chr6:160543347-160543347 | p.Y127C | 2 |
chr6:160560819-160560819 | p.R399H | 2 |
chr6:160555123-160555123 | p.S269A | 2 |
chr6:160551139-160551139 | p.N139H | 2 |
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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 | 2 | 1 | 7 |   |   | 2 |   |   |   |   | 5 | 5 |   |   |   | 7 | 10 |   | 12 |
# mutation | 1 | 2 | 1 | 7 |   |   | 2 |   |   |   |   | 6 | 5 |   |   |   | 7 | 10 |   | 15 |
nonsynonymous SNV |   | 2 | 1 | 6 |   |   | 1 |   |   |   |   | 3 | 4 |   |   |   | 4 | 6 |   | 10 |
synonymous SNV | 1 |   |   | 1 |   |   | 1 |   |   |   |   | 3 | 1 |   |   |   | 3 | 4 |   | 5 |
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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* 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 |
chr6:160555075 | p.A33A,SLC22A1 | 2 |
chr6:160543066 | p.A80S,SLC22A1 | 2 |
chr6:160543205 | p.G253W,SLC22A1 | 2 |
chr6:160560827 | p.R402C,SLC22A1 | 2 |
chr6:160557608 | p.V191M,SLC22A1 | 1 |
chr6:160542971 | p.T327T,SLC22A1 | 1 |
chr6:160543354 | p.L464L | 1 |
chr6:160564597 | p.P197P,SLC22A1 | 1 |
chr6:160557644 | p.K329N,SLC22A1 | 1 |
chr6:160543054 | p.S470F | 1 |
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* 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. |
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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 SLC22A1 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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APOA1,APOA2,APOC3,ASGR1,ASGR2,CA5A,CATSPER1, F2,HP,HRG,ITIH1,KNG1,LEAP2,MT1M, PLG,SERPINC1,SLC22A1,SLC22A7,SLC2A2,SPP2,SULT2A1 | C3orf35,CDH7,FUT9,HAO2,IL1RAPL1,KCNU1,KIAA1875, KRT26,LOC146880,LOC642846,MAGEC2,RANBP17,RLN2,RNF207, RPGRIP1,SLC22A1,SNORA4,SOX14,STXBP5L,TEX14,ZPLD1 | ||||
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ACRC,ACSS3,C6orf164,LINC00518,DNAH1,GPR45,KCNC2, PSMG3-AS1,KLRF1,KRTAP5-9,LINC00685,OR1S1,OR6F1,PSG10P, RBM6,RNF113B,RPL13P5,SLC22A14,SLC22A1,TRIM48,TRIM63 | ADH7,AMTN,CSN1S1,CT83,PRR32,DUSP13,GAGE12J, IQCD,KRT34,KRTAP4-7,LCE1F,LCE4A,NQO1,OASL, SERPINB13,SERPINB4,SLC22A1,SLC25A33,SSX1,SSX2,TMPRSS11A |
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* 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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Pharmacological Information for SLC22A1 |
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DB Category | DB Name | DB's ID and Url link |
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* Gene Centered Interaction Network. |
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* 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 1 | approved | Metformin | ![]() | ![]() |
DB00193 | solute carrier family 22 (organic cation transporter), member 1 | approved; investigational | Tramadol | ![]() | ![]() |
DB00619 | solute carrier family 22 (organic cation transporter), member 1 | approved | Imatinib | ![]() | ![]() |
DB00958 | solute carrier family 22 (organic cation transporter), member 1 | approved | Carboplatin | ![]() | ![]() |
DB00515 | solute carrier family 22 (organic cation transporter), member 1 | approved | Cisplatin | ![]() | ![]() |
DB00526 | solute carrier family 22 (organic cation transporter), member 1 | approved; investigational | Oxaliplatin | ![]() | ![]() |
DB00321 | solute carrier family 22 (organic cation transporter), member 1 | approved | Amitriptyline | ![]() | ![]() |
DB00661 | solute carrier family 22 (organic cation transporter), member 1 | approved | Verapamil | ![]() | ![]() |
DB01045 | solute carrier family 22 (organic cation transporter), member 1 | approved | Rifampin | ![]() | ![]() |
DB00787 | solute carrier family 22 (organic cation transporter), member 1 | approved | Aciclovir | ![]() | ![]() |
DB00879 | solute carrier family 22 (organic cation transporter), member 1 | approved; investigational | Emtricitabine | ![]() | ![]() |
DB00709 | solute carrier family 22 (organic cation transporter), member 1 | approved; investigational | Lamivudine | ![]() | ![]() |
DB00495 | solute carrier family 22 (organic cation transporter), member 1 | approved | Zidovudine | ![]() | ![]() |
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Cross referenced IDs for SLC22A1 |
* 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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