|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SLC23A1 |
Basic gene info. | Gene symbol | SLC23A1 |
Gene name | solute carrier family 23 (ascorbic acid transporter), member 1 | |
Synonyms | SLC23A2|SVCT1|YSPL3 | |
Cytomap | UCSC genome browser: 5q31.2 | |
Genomic location | chr5 :138702884-138719039 | |
Type of gene | protein-coding | |
RefGenes | NM_005847.4, NM_152685.3, | |
Ensembl id | ENSG00000170482 | |
Description | Na(+)/L-ascorbic acid transporter 1hSVCT1sodium-dependent vitamin C transporter 1sodium-dependent vitamin C transporter-1solute carrier family 23 (nucleobase transporters), member 1solute carrier family 23 (nucleobase transporters), member 2solute c | |
Modification date | 20141222 | |
dbXrefs | MIM : 603790 | |
HGNC : HGNC | ||
Ensembl : ENSG00000170482 | ||
HPRD : 04810 | ||
Vega : OTTHUMG00000129228 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SLC23A1 | |
BioGPS: 9963 | ||
Gene Expression Atlas: ENSG00000170482 | ||
The Human Protein Atlas: ENSG00000170482 | ||
Pathway | NCI Pathway Interaction Database: SLC23A1 | |
KEGG: SLC23A1 | ||
REACTOME: SLC23A1 | ||
ConsensusPathDB | ||
Pathway Commons: SLC23A1 | ||
Metabolism | MetaCyc: SLC23A1 | |
HUMANCyc: SLC23A1 | ||
Regulation | Ensembl's Regulation: ENSG00000170482 | |
miRBase: chr5 :138,702,884-138,719,039 | ||
TargetScan: NM_005847 | ||
cisRED: ENSG00000170482 | ||
Context | iHOP: SLC23A1 | |
cancer metabolism search in PubMed: SLC23A1 | ||
UCL Cancer Institute: SLC23A1 | ||
Assigned class in ccmGDB | C |
Top |
Phenotypic Information for SLC23A1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SLC23A1 |
Familial Cancer Database: SLC23A1 |
* 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_METABOLISM_OF_VITAMINS_AND_COFACTORS |
Mutations for SLC23A1 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SLC23A1 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 |
Top |
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 |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
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) |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=38) | (# total SNVs=21) |
(# total SNVs=0) | (# total SNVs=3) |
Top |
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 |
chr5:138717666-138717666 | p.D75N | 2 |
chr5:138714888-138714888 | p.? | 2 |
chr5:138713181-138713181 | p.L491V | 2 |
chr5:138713965-138713966 | p.L423fs*7 | 2 |
chr5:138707828-138707828 | p.R559K | 2 |
chr5:138715727-138715727 | p.R233H | 2 |
chr5:138718265-138718265 | p.P22P | 2 |
chr5:138717662-138717662 | p.Q76L | 1 |
chr5:138707712-138707712 | p.V598M | 1 |
chr5:138714357-138714357 | p.G368S | 1 |
Top |
SNV Counts per Each Loci in TCGA data |
|
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 |   | 14 | 1 |   | 3 |   | 5 |   |   | 3 | 2 | 1 |   |   | 4 | 7 |   | 10 |
# mutation |   | 2 |   | 15 | 1 |   | 3 |   | 5 |   |   | 3 | 2 | 1 |   |   | 4 | 7 |   | 12 |
nonsynonymous SNV |   | 2 |   | 10 | 1 |   | 3 |   | 4 |   |   |   | 2 | 1 |   |   | 4 | 4 |   | 7 |
synonymous SNV |   |   |   | 5 |   |   |   |   | 1 |   |   | 3 |   |   |   |   |   | 3 |   | 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]) |
Top |
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 |
chr5:138717666 | p.P22P,SLC23A1 | 2 |
chr5:138718265 | p.D75N,SLC23A1 | 2 |
chr5:138707712 | p.F29L,SLC23A1 | 1 |
chr5:138715467 | p.D577N,SLC23A1 | 1 |
chr5:138713128 | p.T412S,SLC23A1 | 1 |
chr5:138717642 | p.I261M,SLC23A1 | 1 |
chr5:138714984 | p.K576K,SLC23A1 | 1 |
chr5:138707763 | p.G371G,SLC23A1 | 1 |
chr5:138715509 | p.F255F,SLC23A1 | 1 |
chr5:138713670 | p.R229L,SLC23A1 | 1 |
Other DBs for Point Mutations |
Copy Number for SLC23A1 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] |
Top |
Gene Expression for SLC23A1 |
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)) |
Top |
CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
Top |
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 |
AMY1A,BPIFB2,C15orf27,ZBED6CL,CASP14,CCL25,CSAG3, FLJ34503,GABRA1,GBP7,KRT33B,LOC400759,ORM2,OSTalpha, PRSS55,PSORS1C2,SDR9C7,SFTPD,SLC23A1,UBE2L6,ZNF703 | ATG16L1,AUTS2,C20orf96,CA8,CACNA1D,CELSR1,EDARADD, FLJ46111,FOXA1,HKR1,IQCH,LOC100130093,LRRC48,MORN4, RALGPS1,RPS10P7,SLC23A1,SLITRK6,SMPD3,STC2,TBC1D9 | ||||
A1CF,ABCC6,ABCC6P1,ACE2,AGT,SMIM24,CLCN5, DHRS11,FAH,LRRC43,MMEL1,SLC51B,PKLR,RBP2, SERPINA7,SFXN5,SGK2,SLC13A2,SLC23A1,SLC23A3,SLC39A5 | ACE2,CHN2,CYP2C9,CYP4F2,DHDH,DPP4,FGF19, G6PC,HAPLN4,HSD3B1,MEP1B,MS4A10,NAT8B,SLC23A1, SLC6A4,SULT1E1,TM6SF2,AGMO,TREH,UGT1A4,XPNPEP2 |
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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for SLC23A1 |
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 |
DB00126 | solute carrier family 23 (nucleobase transporters), member 1 | approved; nutraceutical | Vitamin C |
Top |
Cross referenced IDs for SLC23A1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |