Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	SLC23A2
	Gene name	solute carrier family 23 (ascorbic acid transporter), member 2
	Synonyms	NBTL1\|SLC23A1\|SVCT2\|YSPL2
	Cytomap	UCSC genome browser: 20p13
	Genomic location	chr20 :4833001-4990939
	Type of gene	protein-coding
	RefGenes	NM_005116.5, NM_203327.1,
	Ensembl id	ENSG00000089057
	Description	Na(+)/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 date	20141222
dbXrefs	MIM : 603791
	HGNC : HGNC
	Ensembl : ENSG00000089057
	HPRD : 04811
	Vega : OTTHUMG00000031793
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLC23A2
	BioGPS: 9962
	Gene Expression Atlas: ENSG00000089057
	The Human Protein Atlas: ENSG00000089057
Pathway	NCI Pathway Interaction Database: SLC23A2
	KEGG: SLC23A2
	REACTOME: SLC23A2
	ConsensusPathDB
	Pathway Commons: SLC23A2
Metabolism	MetaCyc: SLC23A2
	HUMANCyc: SLC23A2
Regulation	Ensembl's Regulation: ENSG00000089057
	miRBase: chr20 :4,833,001-4,990,939
	TargetScan: NM_005116
	cisRED: ENSG00000089057
Context	iHOP: SLC23A2
	cancer metabolism search in PubMed: SLC23A2
	UCL Cancer Institute: SLC23A2
Assigned class in ccmGDB	C

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Phenotypic Information for SLC23A2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS

Others
OMIM
Orphanet
Disease	KEGG Disease: SLC23A2
	MedGen: SLC23A2 (Human Medical Genetics with Condition)
	ClinVar: SLC23A2
Phenotype	MGI: SLC23A2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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
ovary	SLC23A2	chr20	4891940	4891960	SLC23A2	chr20	4859575	4859595
ovary	SLC23A2	chr20	4926518	4926538	SLC23A2	chr20	4922869	4922889

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 SLC23A2 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
BF088490	FLOT2	6	241	17	27208983	27209407	SLC23A2	230	353	20	4943158	4943281
BM708210	SLC23A2	1	117	20	4835006	4835122	NDUFS2	114	163	1	161184136	161184185
BF923492	SLC23A2	13	379	20	4864418	4880357	SLC23A2	377	435	20	4883113	4883171
BF805458	UBC	12	217	12	125398070	125398278	SLC23A2	211	399	20	4833041	4833227
AI497603	RPL36	24	66	19	5691636	5691678	SLC23A2	65	335	20	4833667	4833937

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=5

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Somatic 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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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
chr20:4850569-4850569	p.I412fs*4	5
chr20:4854682-4854682	p.D334D	5
chr20:4864313-4864313	p.G267R	3
chr20:4843470-4843470	p.A480A	2
chr20:4848512-4848512	p.F420F	2
chr20:4850563-4850563	p.H413Q	2
chr20:4843493-4843493	p.G473W	2
chr20:4837800-4837800	p.G591W	2
chr20:4855319-4855319	p.F283S	1
chr20:4913102-4913102	p.P36Q	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2			12			8		4	1		7	4	3		1	4	12	1	9
# mutation	2			12			8		4	1		8	4	3		1	4	13	1	10
nonsynonymous SNV				9			5		2	1		5	4	3			3	9	1	7
synonymous SNV	2			3			3		2			3				1	1	4		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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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
chr20:4864313	p.G267R,SLC23A2	2
chr20:4848512	p.G591W,SLC23A2	2
chr20:4837800	p.V588L,SLC23A2	2
chr20:4837809	p.F420F,SLC23A2	2
chr20:4866479	p.P410H,SLC23A2	1
chr20:4843520	p.F283S,SLC23A2	1
chr20:4854621	p.R161S,SLC23A2	1
chr20:4880333	p.G21D,SLC23A2	1
chr20:4839999	p.T556N,SLC23A2	1
chr20:4866508	p.R403L,SLC23A2	1

Other 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

Copy 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

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.

: Open all plots for all cancer types

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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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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