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 SLC23A2
Basic gene info.Gene symbolSLC23A2
Gene namesolute carrier family 23 (ascorbic acid transporter), member 2
SynonymsNBTL1|SLC23A1|SVCT2|YSPL2
CytomapUCSC genome browser: 20p13
Genomic locationchr20 :4833001-4990939
Type of geneprotein-coding
RefGenesNM_005116.5,
NM_203327.1,
Ensembl idENSG00000089057
DescriptionNa(+)/L-ascorbic acid transporter 2hSVCT2nucleobase transporter-like 1 proteinsodium-dependent vitamin C transporter-2solute carrier family 23 (nucleobase transporters), member 1solute carrier family 23 (nucleobase transporters), member 2solute carr
Modification date20141222
dbXrefs MIM : 603791
HGNC : HGNC
Ensembl : ENSG00000089057
HPRD : 04811
Vega : OTTHUMG00000031793
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC23A2
BioGPS: 9962
Gene Expression Atlas: ENSG00000089057
The Human Protein Atlas: ENSG00000089057
PathwayNCI Pathway Interaction Database: SLC23A2
KEGG: SLC23A2
REACTOME: SLC23A2
ConsensusPathDB
Pathway Commons: SLC23A2
MetabolismMetaCyc: SLC23A2
HUMANCyc: SLC23A2
RegulationEnsembl's Regulation: ENSG00000089057
miRBase: chr20 :4,833,001-4,990,939
TargetScan: NM_005116
cisRED: ENSG00000089057
ContextiHOP: SLC23A2
cancer metabolism search in PubMed: SLC23A2
UCL Cancer Institute: SLC23A2
Assigned class in ccmGDBC

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Phenotypic Information for SLC23A2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC23A2
Familial Cancer Database: SLC23A2
* 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SLC23A2
MedGen: SLC23A2 (Human Medical Genetics with Condition)
ClinVar: SLC23A2
PhenotypeMGI: SLC23A2 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC23A2

Mutations for SLC23A2
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovarySLC23A2chr2048919404891960SLC23A2chr2048595754859595
ovarySLC23A2chr2049265184926538SLC23A2chr2049228694922889
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SLC23A2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF088490FLOT26241172720898327209407SLC23A22303532049431584943281
BM708210SLC23A211172048350064835122NDUFS21141631161184136161184185
BF923492SLC23A2133792048644184880357SLC23A23774352048831134883171
BF805458UBC1221712125398070125398278SLC23A22113992048330414833227
AI497603RPL3624661956916365691678SLC23A2653352048336674833937

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
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)

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check002.gifSNV 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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=42)
Stat. for Synonymous SNVs
(# total SNVs=19)
Stat. for Deletions
(# total SNVs=9)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr20:4854682-4854682p.D334D5
chr20:4850569-4850569p.I412fs*45
chr20:4864313-4864313p.G267R3
chr20:4837800-4837800p.G591W2
chr20:4843470-4843470p.A480A2
chr20:4848512-4848512p.F420F2
chr20:4850563-4850563p.H413Q2
chr20:4843493-4843493p.G473W2
chr20:4913169-4913169p.E14K1
chr20:4843515-4843515p.L465L1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  12  8 41 743 141219
# mutation2  12  8 41 843 1413110
nonsynonymous SNV   9  5 21 543  3917
synonymous SNV2  3  3 2  3   114 3
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr20:4837800p.G591W,SLC23A22
chr20:4837809p.V588L,SLC23A22
chr20:4864313p.F420F,SLC23A22
chr20:4848512p.G267R,SLC23A22
chr20:4850573p.E55E,SLC23A21
chr20:4866555p.G473W,SLC23A21
chr20:4855238p.L310Q,SLC23A21
chr20:4893568p.T189I,SLC23A21
chr20:4842670p.G47S,SLC23A21
chr20:4864398p.A464S,SLC23A21

check002.gifOther 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

check002.gifCopy Number for SLC23A2 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 SLC23A2

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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

ATRN,BPTF,GPATCH2L,C20orf194,CRYBA1,CSNK2A3,DEFB127,
DMXL1,CCSER1,HRNR,MAVS,N4BP2,NR2C2,PCNX,
PLEKHM3,PPFIA2,PRKCA,RBFOX2,SLC23A2,TBC1D5,ZHX3
ANKFY1,ANKRD36BP1,BBX,BTBD7,FAM208A,CCDC93,CNOT1,
DOCK1,AGO1,KIAA0430,KIDINS220,LOC100132707,MGAT5,NR2C2,
NUMB,SLC23A2,TBC1D5,USP34,ZNF347,ZNF354C,ZNF621

ABI3BP,ADARB1,ATRN,CARD8,DCAF5,DSTYK,HERC1,
HIP1,INPP4A,IQSEC1,ITPKB,KCND1,MEGF8,MFNG,
PCNX,PDE7B,PHF21A,PPM1F,SLC23A2,SLC41A1,USP51
ARHGAP31,ASAP1,ASXL1,CCDC149,CHD6,HIP1,IQSEC1,
MCC,MTR,NOTCH2,OBSCN,PHF2,PODXL,REV3L,
SLC23A2,SSH1,SYNGAP1,WDR91,ZNF337,ZNF445,ZNF589
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting 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 SLC23A2


There's no related Drug.
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Cross referenced IDs for SLC23A2
* 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



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