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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 SYCP1
check button Gene summary
Basic gene informationGene symbolSYCP1
Gene namesynaptonemal complex protein 1
SynonymsCT8|HOM-TES-14|SCP-1|SCP1
CytomapUCSC genome browser: 1p13-p12
Type of geneprotein-coding
RefGenesNM_001282541.1,
NM_001282542.1,NM_003176.3,NR_104211.1,
Descriptioncancer/testis antigen 8
Modification date20141207
dbXrefs MIM : 602162
HGNC : HGNC
Ensembl : ENSG00000198765
HPRD : 03698
Vega : OTTHUMG00000012057
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SYCP1
BioGPS: 6847
PathwayNCI Pathway Interaction Database: SYCP1
KEGG: SYCP1
REACTOME: SYCP1
Pathway Commons: SYCP1
ContextiHOP: SYCP1
ligand binding site mutation search in PubMed: SYCP1
UCL Cancer Institute: SYCP1
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)Testis
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)TGCT
Reference showing the relevant tissue of SYCP1A promoter fragment of the sycp1 gene is sufficient to drive transgene expression in male and female meiotic germ cells in zebrafish. Biol Reprod. 2013 Oct 17;89(4):89. doi: 10.1095/biolreprod.113.107706. Print 2013 Oct. (pmid:23966324)
go to article
Description by TissGene annotationsTissgsKTS
CNV lost TissGeneKTS
* 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 SYCP1

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


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TissGene-miRNA for SYCP1

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 SYCP1
TissGeneSNV for SYCP1

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.R882KSKCM5
p.S374LSKCM2
p.W119XSKCM2
p.W808*SKCM2
p.E515KSKCM2
p.E509KSKCM2
p.E60KSKCM2
p.W119*SKCM2
p.P850LSKCM1
p.T337NUCEC1
p.L594VUCS1
p.G462ESKCM1
p.E435*UCEC1
p.R955HSKCM1
p.E442KSKCM1
p.I673MLGG1
p.E411XCOAD1
p.L467RCOAD1
p.D700NSKCM1
p.E775KSKCM1
p.D403AUCEC1
p.Q413*SKCM1
p.T423SLIHC1
p.R587IUCEC1
p.L228VLUAD1
p.E279KUCEC1
p.R236SSTAD1
p.D284YUCEC1
p.Q26ECESC1
p.N612KLUAD1
p.E507GREAD1
p.N297KLUSC1
p.L511PSKCM1
p.L502IREAD1
p.Y110CLIHC1
p.S743LCOAD1
p.R822XSKCM1
p.E435DCOAD1
p.T445IBRCA1
p.S941FSKCM1
p.E759XKIRC1
p.I327NSKCM1
p.N918HCOAD1
p.R702XREAD1
p.E290DBLCA1
p.K642_spliceUCEC1
p.V687LUCS1
p.V384LSTAD1
p.E256*UCEC1
p.A147PHNSC1
p.K220NSTAD1
p.R771IREAD1
p.K497NSKCM1
p.S366FSTAD1
p.P49SSKCM1
p.I222VKICH1
p.I707RDLBC1
p.R392ICOAD1
p.E411KHNSC1
p.P804HLUAD1
p.E315KSKCM1
p.Q585HSKCM1
p.Q655HREAD1
p.Q26HESCA1
p.K880*HNSC1
p.E759*KIRC1
p.A689SSARC1
p.E972KBLCA1
p.E482KSKCM1
p.R964KESCA1
p.K92NCOAD1
p.R952PLUSC1
p.E379KSKCM1
p.E731KSKCM1
p.E323XREAD1
p.R474KLUAD1
p.L523VLUAD1
p.R145LLUSC1
p.R229CSKCM1
p.Q79_spliceLUSC1
p.R822*SKCM1
p.L713FLIHC1
p.R702QGBM1
p.S374*UCEC1
p.S832FBLCA1
p.E970GLUAD1
p.M962IUCEC1
p.E248*SARC1
p.P939SSKCM1
p.Q766KPRAD1
p.G101RSKCM1
p.E131KSKCM1
p.L936VSTAD1
p.P25LHNSC1
p.K350TUCEC1
p.S744LSTAD1
p.A67VSKCM1
p.R702QSKCM1
p.R955HCOAD1
p.E563*UCEC1
p.S417ROV1
p.S535RCOAD1
p.R771KHNSC1
p.A371TLGG1
p.Y914NHNSC1
p.E498QBLCA1
p.E454GLGG1
p.E399KESCA1
p.G830DLGG1
p.R229SLUAD1
p.H829QLUSC1
p.E168XREAD1
p.L974XESCA1
p.L756FSKCM1
p.E364QKIRP1
p.T207ISTAD1
p.M962ISKCM1
p.K400NREAD1
p.L974*ESCA1
p.Q566ELUAD1
p.R204WPAAD1
p.E617*UCEC1
p.R952WUCEC1
p.L871FBLCA1
p.S496LBRCA1
p.D213NSKCM1
p.K642NUCEC1
p.S842FBLCA1
p.R229HSTAD1
p.R952GLUAD1
p.H373DCESC1
p.S812YCOAD1
p.N401HCOAD1
p.W808XSKCM1
p.K242TSTAD1
p.S826LLIHC1
p.S754FSKCM1
p.S524LSKCM1
p.P75LCOAD1
p.E290QBRCA1
p.L810SSKCM1
p.R702*SARC1
p.P816SSKCM1
p.E343XESCA1
p.K451EBLCA1
p.E449*UCEC1
p.A631TUCEC1
p.E459*UCEC1
p.E581KBLCA1
p.H318NLUAD1
p.F888LSKCM1
p.T517AHNSC1
p.F886ILIHC1
p.E2DHNSC1
p.R587KSKCM1
p.R474KSKCM1
p.L270QOV1
p.E556KHNSC1
p.E556KSKCM1
p.K757NLUAD1
p.K339NLUAD1
p.E680*LUAD1
p.L900RSTAD1
p.E675KSKCM1
p.E444KSKCM1
p.D793NSKCM1
p.D31NHNSC1
p.D722NSKCM1
p.Q867KLUAD1
p.R952QLUSC1


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TissGeneCNV for SYCP1

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 SYCP1

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
Chimerdb3.0ChiTaRsNAAW393520DYNC1LI2-SYCP1chr16:66756246chr1:115520197


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TissGeneNet for SYCP1

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)
SYCP1, UBC (tumor)SYCP1, UBC (normal)
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COAD (tumor)COAD (normal)
SYCP1, UBC (tumor)SYCP1, UBC (normal)
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HNSC (tumor)HNSC (normal)
SYCP1, UBC (tumor)SYCP1, UBC (normal)
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KICH (tumor)KICH (normal)
SYCP1, UBC (tumor)SYCP1, UBC (normal)
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KIRC (tumor)KIRC (normal)
SYCP1, UBC (tumor)SYCP1, UBC (normal)
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KIRP (tumor)KIRP (normal)
SYCP1, UBC (tumor)SYCP1, UBC (normal)
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LIHC (tumor)LIHC (normal)
SYCP1, UBC (tumor)SYCP1, UBC (normal)
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LUAD (tumor)LUAD (normal)
SYCP1, UBC (tumor)SYCP1, UBC (normal)
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LUSC (tumor)LUSC (normal)
SYCP1, UBC (tumor)SYCP1, UBC (normal)
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PRAD (tumor)PRAD (normal)
SYCP1, UBC (tumor)SYCP1, UBC (normal)
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STAD (tumor)STAD (normal)
SYCP1, UBC (tumor)SYCP1, UBC (normal)
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THCA (tumor)THCA (normal)
SYCP1, UBC (tumor)SYCP1, UBC (normal)
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TissGeneProg for SYCP1

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 SYCP1
TissGeneDrug for SYCP1

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 SYCP1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0153594Malignant neoplasm of testis4BeFree
umls:C0079773Lymphoma, T-Cell, Cutaneous2BeFree
umls:C0001418Adenocarcinoma1CTD_human
umls:C0004509Azoospermia1GAD
umls:C0006142Malignant neoplasm of breast1BeFree
umls:C0023470Myeloid Leukemia1BeFree
umls:C0023473Myeloid Leukemia, Chronic1BeFree
umls:C0026764Multiple Myeloma1BeFree
umls:C0028960Oligospermia1GAD
umls:C0030297Pancreatic Neoplasm1CTD_human
umls:C0030491Parapsoriasis1BeFree
umls:C0039101synovial sarcoma1BeFree
umls:C0043346Xeroderma Pigmentosum1BeFree
umls:C0279702Conventional (Clear Cell) Renal Cell Carcinoma1BeFree
umls:C0678222Breast Carcinoma1BeFree
umls:C2745900Promyelocytic leukemia1BeFree