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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 TSPAN1
check button Gene summary
Basic gene informationGene symbolTSPAN1
Gene nametetraspanin 1
SynonymsNET1|TM4C|TM4SF
CytomapUCSC genome browser: 1p34.1
Type of geneprotein-coding
RefGenesNM_005727.3,
Descriptiontetraspan 1tetraspanin-1
Modification date20141207
dbXrefs MIM : 613170
HGNC : HGNC
Ensembl : ENSG00000117472
HPRD : 18232
Vega : OTTHUMG00000007602
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TSPAN1
BioGPS: 10103
PathwayNCI Pathway Interaction Database: TSPAN1
KEGG: TSPAN1
REACTOME: TSPAN1
Pathway Commons: TSPAN1
ContextiHOP: TSPAN1
ligand binding site mutation search in PubMed: TSPAN1
UCL Cancer Institute: TSPAN1
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)ColonKidney
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)COADKIRC,KIRP,KICH
Reference showing the relevant tissue of TSPAN1
Description by TissGene annotationsProtective TissGene in OS
* 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
GO:0008283cell proliferation22378020
GO:0050821protein stabilization21836059
GO:0071934thiamine transmembrane transport21836059
GO:0008283cell proliferation22378020
GO:0050821protein stabilization21836059
GO:0071934thiamine transmembrane transport21836059


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TissGeneExp for TSPAN1

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
COAD3.5595159676.027758275-2.4682423084.45E-117.07E-10
PRAD5.6699601984.2495948131.4203653852.53E-117.00E-10
KIRC2.4450349844.018025262-1.5729902781.18E-083.56E-08
BRCA1.002414078-0.6853736421.6877877193.02E-101.14E-09
KICH1.3913344283.932562428-2.5412281.91E-091.14E-08
LUSC0.5719210951.597142664-1.0252215690.004250.007190834


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TissGene-miRNA for TSPAN1

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


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TissGeneMut for TSPAN1
TissGeneSNV for TSPAN1

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.G74RESCA1
p.I126MBRCA1
p.L240VBLCA1
p.M11VKIRC1
p.G146WUCEC1
p.V218ASKCM1
p.V66ALUSC1
p.T119ABLCA1
p.T119MCOAD1
p.D35NLUAD1
p.E226KSKCM1
p.P171LLGG1
p.Y130HSTAD1


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TissGeneCNV for TSPAN1

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 TSPAN1

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
TCGAfusionPortalPRADAPRADTCGA-G9-6371-01ATSPAN1-USP203UTR-CDSChr1:46651630Chr9:132620746
TCGAfusionPortalPRADAPRADTCGA-HC-7738-01ATSPAN1-TFF33UTR-5UTRChr1:46651630Chr21:43735706


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TissGeneNet for TSPAN1

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)
TSPAN1, NFKBIB, MDK (tumor)TSPAN1, NFKBIB, MDK (normal)
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COAD (tumor)COAD (normal)
TSPAN1, NFKBIB, MDK (tumor)TSPAN1, NFKBIB, MDK (normal)
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HNSC (tumor)HNSC (normal)
TSPAN1, NFKBIB, MDK (tumor)TSPAN1, NFKBIB, MDK (normal)
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KICH (tumor)KICH (normal)
TSPAN1, NFKBIB, MDK (tumor)TSPAN1, NFKBIB, MDK (normal)
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KIRC (tumor)KIRC (normal)
TSPAN1, NFKBIB, MDK (tumor)TSPAN1, NFKBIB, MDK (normal)
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KIRP (tumor)KIRP (normal)
TSPAN1, NFKBIB, MDK (tumor)TSPAN1, NFKBIB, MDK (normal)
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LIHC (tumor)LIHC (normal)
TSPAN1, NFKBIB, MDK (tumor)TSPAN1, NFKBIB, MDK (normal)
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LUAD (tumor)LUAD (normal)
TSPAN1, NFKBIB, MDK (tumor)TSPAN1, NFKBIB, MDK (normal)
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LUSC (tumor)LUSC (normal)
TSPAN1, NFKBIB, MDK (tumor)TSPAN1, NFKBIB, MDK (normal)
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PRAD (tumor)PRAD (normal)
TSPAN1, NFKBIB, MDK (tumor)TSPAN1, NFKBIB, MDK (normal)
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STAD (tumor)STAD (normal)
TSPAN1, NFKBIB, MDK (tumor)TSPAN1, NFKBIB, MDK (normal)
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THCA (tumor)THCA (normal)
TSPAN1, NFKBIB, MDK (tumor)TSPAN1, NFKBIB, MDK (normal)
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TissGeneProg for TSPAN1

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 TSPAN1
TissGeneDrug for TSPAN1

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status


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TissGeneDisease for TSPAN1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0027627Neoplasm Metastasis6BeFree
umls:C0699791Stomach Carcinoma5BeFree
umls:C2239176Liver carcinoma5BeFree,LHGDN
umls:C0001418Adenocarcinoma4BeFree
umls:C0006142Malignant neoplasm of breast4BeFree
umls:C0024623Malignant neoplasm of stomach4BeFree
umls:C0278701Gastric Adenocarcinoma4BeFree
umls:C0678222Breast Carcinoma4BeFree
umls:C1263846Attention deficit hyperactivity disorder4BeFree
umls:C0007137Squamous cell carcinoma2BeFree,LHGDN
umls:C0009402Colorectal Carcinoma2BeFree
umls:C0011436Dentinogenesis Imperfecta2BeFree
umls:C0553723Squamous cell carcinoma of skin2BeFree
umls:C1261473Sarcoma2BeFree
umls:C0006118Brain Neoplasms1BeFree
umls:C0007873Uterine Cervical Neoplasm1LHGDN
umls:C0011311Dengue Fever1BeFree
umls:C0011430Dentin Dysplasia1BeFree
umls:C0011849Diabetes Mellitus1GAD
umls:C0011860Diabetes Mellitus, Non-Insulin-Dependent1GAD
umls:C0029121Oppositional Defiant Disorder1BeFree
umls:C0178874Tumor Progression1BeFree
umls:C0206708Cervical Intraepithelial Neoplasia1BeFree
umls:C0235974Pancreatic carcinoma1BeFree
umls:C0278488Carcinoma breast stage IV1BeFree
umls:C0280100Solid tumour1BeFree
umls:C0346647Malignant neoplasm of pancreas1BeFree
umls:C0546837Malignant neoplasm of esophagus1BeFree
umls:C0596263Carcinogenesis1BeFree