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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for SLC5A6
check button Gene summary
Basic gene informationGene symbolSLC5A6
Gene namesolute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6
SynonymsSMVT
CytomapUCSC genome browser: 2p23
Type of geneprotein-coding
RefGenesNM_021095.2,
NR_028323.1,
DescriptionNa(+)-dependent multivitamin transporterNa+-dependent multivitamin transportersodium-dependent multivitamin transportersolute carrier family 5 (sodium-dependent vitamin transporter), member 6solute carrier family 5 member 6
Modification date20141211
dbXrefs MIM : 604024
HGNC : HGNC
Ensembl : ENSG00000138074
HPRD : 04934
Vega : OTTHUMG00000097075
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC5A6
BioGPS: 8884
PathwayNCI Pathway Interaction Database: SLC5A6
KEGG: SLC5A6
REACTOME: SLC5A6
Pathway Commons: SLC5A6
ContextiHOP: SLC5A6
ligand binding site mutation search in PubMed: SLC5A6
UCL Cancer Institute: SLC5A6
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)LiverStomach
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LIHCSTAD
Reference showing the relevant tissue of SLC5A6
Description by TissGene annotationsCancer gene
TissgsLTS
Fused withOncogene
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID


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TissGeneExp for SLC5A6

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
COAD2.7771725381.2721417681.5050307692.09E-124.87E-11
LUAD1.2876421660.1585404421.1291017248.99E-264.20E-24
STAD1.9564893650.520511241.4359781254.68E-092.77E-07
BLCA2.2283008780.5161640361.7121368422.40E-081.84E-06
LUSC1.9648779670.2844720851.6804058821.29E-201.64E-19
ESCA2.1065410690.6266683421.4798727270.0001870.005010699


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TissGene-miRNA for SLC5A6

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples
UVMhsa-let-7b-5pMIMAT00000630.01-0.2980


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TissGeneMut for SLC5A6
TissGeneSNV for SLC5A6

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)

* Click on the image to enlarge it in a new window.
SNV lollipop
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.V83MCOAD1
p.R123HHNSC1
p.P574TTHYM1
p.A198VCOAD1
p.G405DGBM1
p.E389KLUAD1
p.G239DSTAD1
p.V341LLUAD1
p.R53WPRAD1
p.S15WLUAD1
p.R136XSTAD1
p.R142*CESC1
p.R136QCOAD1
p.I475TSTAD1
p.M397VSTAD1
p.S12FSKCM1
p.F24LUCS1
p.V160EKIRC1
p.V501ISTAD1
p.W51*CESC1
p.G362SUCEC1
p.R553*UCEC1
p.G405VBLCA1
p.D334YSTAD1
p.Y29CCOAD1
p.S236PSTAD1
p.T500IUCEC1
p.S39CBLCA1
p.D592NSTAD1
p.T127SLUAD1
p.Y530*STAD1
p.S8*BLCA1
p.L44RBRCA1
p.F522LCESC1
p.A317VKIRP1
p.R384LLUSC1
p.R553XREAD1
p.Y530XSTAD1
p.P453SSKCM1
p.P564QESCA1
p.P454HUCEC1
p.G221RSKCM1
p.Q335*SKCM1
p.P574SSKCM1
p.P299SSKCM1
p.A317EESCA1
p.S25FLUSC1
p.V234LBRCA1
p.V217DACC1
p.Y295CKIRP1
p.I219VSKCM1
p.K568RTHYM1
p.R394POV1
p.R136LKIRC1
p.R136*STAD1
p.V120ICOAD1
p.R384QUCEC1
p.Q335XSKCM1
p.S293FSKCM1
p.Q330EBLCA1
p.E131GSTAD1
p.V120ISTAD1
p.P567LOV1
p.L270FLUAD1
p.L411VBRCA1
p.A62VSTAD1
p.D592NCOAD1
p.R64HSTAD1
p.P349SSTAD1


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TissGeneCNV for SLC5A6

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for SLC5A6

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0ChiTaRsNABQ022479RAB11B-SLC5A6chr19:8469213chr2:27423959


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TissGeneNet for SLC5A6

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)
BRCA (tumor)BRCA (normal)
SLC5A6, ERBB2IP, KLF4, GALNT6 (tumor)SLC5A6, ERBB2IP, KLF4, GALNT6 (normal)
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COAD (tumor)COAD (normal)
SLC5A6, ERBB2IP, KLF4, GALNT6 (tumor)SLC5A6, ERBB2IP, KLF4, GALNT6 (normal)
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HNSC (tumor)HNSC (normal)
SLC5A6, ERBB2IP, KLF4, GALNT6 (tumor)SLC5A6, ERBB2IP, KLF4, GALNT6 (normal)
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KICH (tumor)KICH (normal)
SLC5A6, ERBB2IP, KLF4, GALNT6 (tumor)SLC5A6, ERBB2IP, KLF4, GALNT6 (normal)
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KIRC (tumor)KIRC (normal)
SLC5A6, ERBB2IP, KLF4, GALNT6 (tumor)SLC5A6, ERBB2IP, KLF4, GALNT6 (normal)
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KIRP (tumor)KIRP (normal)
SLC5A6, ERBB2IP, KLF4, GALNT6 (tumor)SLC5A6, ERBB2IP, KLF4, GALNT6 (normal)
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LIHC (tumor)LIHC (normal)
SLC5A6, ERBB2IP, KLF4, GALNT6 (tumor)SLC5A6, ERBB2IP, KLF4, GALNT6 (normal)
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LUAD (tumor)LUAD (normal)
SLC5A6, ERBB2IP, KLF4, GALNT6 (tumor)SLC5A6, ERBB2IP, KLF4, GALNT6 (normal)
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LUSC (tumor)LUSC (normal)
SLC5A6, ERBB2IP, KLF4, GALNT6 (tumor)SLC5A6, ERBB2IP, KLF4, GALNT6 (normal)
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PRAD (tumor)PRAD (normal)
SLC5A6, ERBB2IP, KLF4, GALNT6 (tumor)SLC5A6, ERBB2IP, KLF4, GALNT6 (normal)
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STAD (tumor)STAD (normal)
SLC5A6, ERBB2IP, KLF4, GALNT6 (tumor)SLC5A6, ERBB2IP, KLF4, GALNT6 (normal)
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THCA (tumor)THCA (normal)
SLC5A6, ERBB2IP, KLF4, GALNT6 (tumor)SLC5A6, ERBB2IP, KLF4, GALNT6 (normal)
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TissGeneProg for SLC5A6

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for SLC5A6
TissGeneDrug for SLC5A6

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status
DB00121BiotinSmall moleculeApproved|Nutraceutical
DB00166Lipoic AcidSmall moleculeApproved|Nutraceutical


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TissGeneDisease for SLC5A6

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0006142Malignant neoplasm of breast1BeFree
umls:C0011053Deafness1GAD
umls:C0018772Hearing Loss, Partial1GAD
umls:C0079748Precursor cell lymphoblastic lymphoma1BeFree
umls:C0376358Malignant neoplasm of prostate1BeFree
umls:C0600139Prostate carcinoma1BeFree
umls:C0678222Breast Carcinoma1BeFree
umls:C1384666hearing impairment1GAD
umls:C3887873Hearing Loss1GAD