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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 SSX1
check button Gene summary
Basic gene informationGene symbolSSX1
Gene namesynovial sarcoma, X breakpoint 1
SynonymsCT5.1|SSRC
CytomapUCSC genome browser: Xp11.23
Type of geneprotein-coding
RefGenesNM_001278691.1,
NM_005635.3,
Descriptioncancer/testis antigen 5.1cancer/testis antigen family 5, member 1protein SSX1sarcoma, synovial, X-chromosome-related 1
Modification date20141222
dbXrefs MIM : 312820
HGNC : HGNC
Ensembl : ENSG00000126752
HPRD : 02428
Vega : OTTHUMG00000021488
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SSX1
BioGPS: 6756
PathwayNCI Pathway Interaction Database: SSX1
KEGG: SSX1
REACTOME: SSX1
Pathway Commons: SSX1
ContextiHOP: SSX1
ligand binding site mutation search in PubMed: SSX1
UCL Cancer Institute: SSX1
Assigned class in TissGDB*A
Included tissue-specific gene expression resourcesHPA,TiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Bone marrowSkinTestis
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LAMLSKCMTGCT
Reference showing the relevant tissue of SSX1Expression and immunotherapeutic targeting of the SSX family of cancer-testis antigens in prostate cancer.Cancer Res. 2011 Nov 1;71(21):6785-95. doi: 10.1158/0008-5472.CAN-11-2127. (pmid:21880588)
go to article
Description by TissGene annotationsCancer gene
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 SSX1

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
THCA3.4301608450.7116235572.7185372886.36E-135.99E-12
LIHC1.663834303-2.1514696973.8153041.89E-071.24E-06


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TissGene-miRNA for SSX1

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 SSX1
TissGeneSNV for SSX1

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.A8ESKCM1
p.D78NUCEC1
p.E188KSKCM1
p.E184KBLCA1
p.Q133LUCEC1
p.S181ISARC1
p.R169HUCEC1
p.I111FACC1
p.E185KSKCM1
p.P113HTHYM1
p.V94IUCEC1
p.R10ILUSC1
p.R53IUCEC1
p.D27YHNSC1
p.Q80LGBM1
p.D135NKIRP1
p.G143ESKCM1
p.P109TLUAD1
p.A117VSTAD1
p.K23NSTAD1
p.W164CLUAD1
p.E170DCOAD1
p.F79ITHCA1
p.S43LUCEC1
p.M40IHNSC1
p.L168MLIHC1
p.T30KBLCA1
p.P132QLUSC1
p.R12MLGG1


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TissGeneCNV for SSX1

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 SSX1

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
Chimerdb3.0ChiTaRsNAS79325SS18-SSX1chr18:23615074chrX:48123215
Chimerdb3.0ChiTaRsNAAB300355SS18-SSX1chr18:23670542chrX:48123215
Chimerdb3.0ChiTaRsNAAF402618SS18-SSX1chr18:23615029chrX:48123278
Chimerdb3.0FusionScanSARCTCGA-X6-A8C7-01ASS18-SSX1In-Framechr18:23612362chrX:48123216
Chimerdb3.0FusionScanSARCTCGA-DX-A7ER-01ASS18-SSX1In-Framechr18:23612362chrX:48123216
Chimerdb3.0FusionScanSARCTCGA-DX-A7EO-01ASS18-SSX1In-Framechr18:23612362chrX:48123216
Chimerdb3.0FusionScanSARCTCGA-FX-A8OO-01ASS18-SSX1In-Framechr18:23612362chrX:48123216


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TissGeneNet for SSX1

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)
SSX1, SNAI1, CDH1, FUBP3, LHX4 (tumor)SSX1, SNAI1, CDH1, FUBP3, LHX4 (normal)
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COAD (tumor)COAD (normal)
SSX1, SNAI1, CDH1, FUBP3, LHX4 (tumor)SSX1, SNAI1, CDH1, FUBP3, LHX4 (normal)
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HNSC (tumor)HNSC (normal)
SSX1, SNAI1, CDH1, FUBP3, LHX4 (tumor)SSX1, SNAI1, CDH1, FUBP3, LHX4 (normal)
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KICH (tumor)KICH (normal)
SSX1, SNAI1, CDH1, FUBP3, LHX4 (tumor)SSX1, SNAI1, CDH1, FUBP3, LHX4 (normal)
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KIRC (tumor)KIRC (normal)
SSX1, SNAI1, CDH1, FUBP3, LHX4 (tumor)SSX1, SNAI1, CDH1, FUBP3, LHX4 (normal)
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KIRP (tumor)KIRP (normal)
SSX1, SNAI1, CDH1, FUBP3, LHX4 (tumor)SSX1, SNAI1, CDH1, FUBP3, LHX4 (normal)
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LIHC (tumor)LIHC (normal)
SSX1, SNAI1, CDH1, FUBP3, LHX4 (tumor)SSX1, SNAI1, CDH1, FUBP3, LHX4 (normal)
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LUAD (tumor)LUAD (normal)
SSX1, SNAI1, CDH1, FUBP3, LHX4 (tumor)SSX1, SNAI1, CDH1, FUBP3, LHX4 (normal)
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LUSC (tumor)LUSC (normal)
SSX1, SNAI1, CDH1, FUBP3, LHX4 (tumor)SSX1, SNAI1, CDH1, FUBP3, LHX4 (normal)
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PRAD (tumor)PRAD (normal)
SSX1, SNAI1, CDH1, FUBP3, LHX4 (tumor)SSX1, SNAI1, CDH1, FUBP3, LHX4 (normal)
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STAD (tumor)STAD (normal)
SSX1, SNAI1, CDH1, FUBP3, LHX4 (tumor)SSX1, SNAI1, CDH1, FUBP3, LHX4 (normal)
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THCA (tumor)THCA (normal)
SSX1, SNAI1, CDH1, FUBP3, LHX4 (tumor)SSX1, SNAI1, CDH1, FUBP3, LHX4 (normal)
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TissGeneProg for SSX1

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 SSX1
TissGeneDrug for SSX1

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 SSX1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0039101synovial sarcoma57BeFree,CTD_human,LHGDN,ORPHANET
umls:C0027627Neoplasm Metastasis8BeFree
umls:C2239176Liver carcinoma5BeFree
umls:C0153594Malignant neoplasm of testis4BeFree
umls:C1261473Sarcoma4BeFree
umls:C0025202melanoma3BeFree
umls:C0026764Multiple Myeloma2BeFree
umls:C0002395Alzheimer's Disease1GAD
umls:C0023418leukemia1BeFree
umls:C0026470Monoclonal Gammopathy of Undetermined Significance1BeFree
umls:C0031117Peripheral Neuropathy1CTD_human
umls:C0334507Synovial sarcoma, biphasic1BeFree
umls:C0596263Carcinogenesis1BeFree
umls:C1334699Mesenchymal Cell Neoplasm1BeFree
umls:C1520166Xenograft Model1BeFree