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 SLC5A5
Basic gene info.Gene symbolSLC5A5
Gene namesolute carrier family 5 (sodium/iodide cotransporter), member 5
SynonymsNIS|TDH1
CytomapUCSC genome browser: 19p13.11
Genomic locationchr19 :17982781-18005983
Type of geneprotein-coding
RefGenesNM_000453.2,
Ensembl idENSG00000105641
DescriptionNa(+)/I(-) cotransporterNa(+)/I(-) symportersodium/iodide cotransportersolute carrier family 5 (sodium iodide symporter), member 5
Modification date20141207
dbXrefs MIM : 601843
HGNC : HGNC
Ensembl : ENSG00000105641
HPRD : 03504
Vega : OTTHUMG00000183447
ProteinUniProt: Q92911
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC5A5
BioGPS: 6528
Gene Expression Atlas: ENSG00000105641
The Human Protein Atlas: ENSG00000105641
PathwayNCI Pathway Interaction Database: SLC5A5
KEGG: SLC5A5
REACTOME: SLC5A5
ConsensusPathDB
Pathway Commons: SLC5A5
MetabolismMetaCyc: SLC5A5
HUMANCyc: SLC5A5
RegulationEnsembl's Regulation: ENSG00000105641
miRBase: chr19 :17,982,781-18,005,983
TargetScan: NM_000453
cisRED: ENSG00000105641
ContextiHOP: SLC5A5
cancer metabolism search in PubMed: SLC5A5
UCL Cancer Institute: SLC5A5
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SLC5A5 in cancer cell metabolism1. Lacoste C, Hervé J, Nader MB, Dos Santos A, Moniaux N, et al. (2012) Iodide transporter NIS regulates cancer cell motility and invasiveness by interacting with the Rho guanine nucleotide exchange factor LARG. Cancer research 72: 5505-5515. go to article

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Phenotypic Information for SLC5A5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC5A5
Familial Cancer Database: SLC5A5
* 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_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM 274400; phenotype.
601843; gene.
Orphanet 95716; Familial thyroid dyshormonogenesis.
DiseaseKEGG Disease: SLC5A5
MedGen: SLC5A5 (Human Medical Genetics with Condition)
ClinVar: SLC5A5
PhenotypeMGI: SLC5A5 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC5A5

Mutations for SLC5A5
* 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
pancreasSLC5A5chr191799693917996959SLC5A5chr191799715617997176
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 SLC5A5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM690623SYAP18334X1678060316780931SLC5A5326584191800529118005549

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)          1      
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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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=44)
Stat. for Synonymous SNVs
(# total SNVs=23)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr19:18001725-18001725p.G561E3
chr19:17983483-17983483p.E119K3
chr19:18001748-18001748p.R569W2
chr19:17986788-17986788p.D191N2
chr19:17988883-17988883p.R317H2
chr19:17999160-17999160p.R516Q2
chr19:17985478-17985478p.G161R2
chr19:17991703-17991703p.F333F2
chr19:18004596-18004596p.F614F2
chr19:17994765-17994765p.S479L2

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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
# sample241111 5 1  641 112615
# mutation341111 5 1  651 112615
nonsynonymous SNV33191 4 1  22  14513
synonymous SNV 1 2  1    431  81 2
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
chr19:18001748p.F614F2
chr19:17991703p.F333F2
chr19:18004596p.G561E2
chr19:18001725p.A186V2
chr19:17986774p.R569W2
chr19:18001745p.T464M1
chr19:17986820p.P606P1
chr19:18004631p.A128T1
chr19:17988809p.A264A1
chr19:17994525p.V270M1

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 SLC5A5 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 SLC5A5

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

CCDC129,CCDC83,CCR8,CT45A2,DLK1,FAIM2,FZD4,
GABRA2,GADL1,GLYCAM1,GRM7,KRT24,LDLRAD1,OTOR,
PCTP,RXRG,SLC5A5,SULT1E1,SUPT4H1,SYTL2,TCHHL1
BAAT,CDHR2,CELP,CSN1S1,CSN3,GKN2,KRTAP13-1,
NAPSA,PSAPL1,SCGB3A2,SFTA2,SFTA3,SFTPB,SHH,
SLC26A9,SLC5A5,TM4SF20,TM4SF5,TRIM15,TRIM31,ZCCHC16

ARHGAP36,CACNG3,CHRNA4,CHST8,DPYSL5,FLJ36000,GPR50,
HTR1A,NCAN,RNF17,SHISA7,SLC17A6,SLC1A6,SLC5A5,
SLITRK1,TSPY1,X
ANKRD55,CCR6,CCR7,CD37,CD83,CLEC17A,FAIM3,
FAM159A,FCER2,GP1BA,HSF5,IL24,TESPA1,LEF1,
LTB,NCR3,SELL,SLC5A5,TCF7,TREML2,VPREB3
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 SLC5A5
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA35905; -.
Organism-specific databasesCTD 6528; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00135solute carrier family 5 (sodium iodide symporter), member 5approved; nutraceuticalL-Tyrosine
DB00531solute carrier family 5 (sodium iodide symporter), member 5approved; investigationalCyclophosphamide


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Cross referenced IDs for SLC5A5
* 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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