TissGeneSummary for SYCP3 |
Gene summary |
Basic gene information | Gene symbol | SYCP3 |
Gene name | synaptonemal complex protein 3 | |
Synonyms | COR1|SCP3|SPGF4 | |
Cytomap | UCSC genome browser: 12q | |
Type of gene | protein-coding | |
RefGenes | NM_001177948.1, NM_001177949.1,NM_153694.4, | |
Description | - | |
Modification date | 20141207 | |
dbXrefs | MIM : 604759 | |
HGNC : HGNC | ||
Ensembl : ENSG00000139351 | ||
HPRD : 07265 | ||
Vega : OTTHUMG00000150132 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SYCP3 | |
BioGPS: 50511 | ||
Pathway | NCI Pathway Interaction Database: SYCP3 | |
KEGG: SYCP3 | ||
REACTOME: SYCP3 | ||
Pathway Commons: SYCP3 | ||
Context | iHOP: SYCP3 | |
ligand binding site mutation search in PubMed: SYCP3 | ||
UCL Cancer Institute: SYCP3 | ||
Assigned class in TissGDB* | A | |
Included tissue-specific gene expression resources | HPA,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 SYCP3 | Expression of two testis-specific genes, TSGA10 and SYCP3, in different cancers regarding to their pathological features. Cancer Detect Prev. 2007;31(4):296-302. (pmid:17920210) go to article | |
Description by TissGene annotations | TissgsKTS 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. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO term | PubMed ID |
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TissGeneExp for SYCP3 |
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 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 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. |
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) |
- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
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TissGene-miRNA for SYCP3 |
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 type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
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TissGeneMut for SYCP3 |
TissGeneSNV for SYCP3 |
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. |
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) |
- nsSNVs sorted by frequency. |
AAchange | Cancer type | # samples |
p.D194N | STAD | 1 |
p.R155Q | PRAD | 1 |
p.R228W | ACC | 1 |
p.R155Q | UCEC | 1 |
p.L35M | THYM | 1 |
p.V2M | DLBC | 1 |
p.E148* | UCEC | 1 |
p.V227A | LIHC | 1 |
p.E124Q | KIRP | 1 |
p.Q127E | HNSC | 1 |
p.A60E | CESC | 1 |
p.E124Q | BLCA | 1 |
p.R171K | TGCT | 1 |
p.E203* | UCS | 1 |
p.S36T | LUAD | 1 |
p.L85F | STAD | 1 |
p.A209D | UCEC | 1 |
p.K191N | SARC | 1 |
p.E203K | LUAD | 1 |
p.Q135R | KIRP | 1 |
p.E188K | BLCA | 1 |
p.A200V | UCEC | 1 |
p.Y8N | LUAD | 1 |
p.R228Q | UCEC | 1 |
p.Q170L | LIHC | 1 |
p.N82K | GBM | 1 |
p.K191N | BLCA | 1 |
p.M140I | UCEC | 1 |
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TissGeneCNV for SYCP3 |
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) |
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TissGeneFusions for SYCP3 |
Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
Chimerdb3.0 | FusionScan | ESCA | TCGA-JY-A6FH-01A | DRAM1-SYCP3 | Out-of-Frame | chr12:102271698 | chr12:102128822 |
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TissGeneNet for SYCP3 |
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) |
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TissGeneProg for SYCP3 |
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. |
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. |
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. |
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. |
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TissGeneClin for SYCP3 |
TissGeneDrug for SYCP3 |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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TissGeneDisease for SYCP3 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0004509 | Azoospermia | 3 | BeFree,CTD_human,GAD |
umls:C0000809 | Abortion, Habitual | 1 | CTD_human,LHGDN |
umls:C0007847 | Malignant tumor of cervix | 1 | BeFree |
umls:C0023467 | Leukemia, Myelocytic, Acute | 1 | BeFree |
umls:C0023470 | Myeloid Leukemia | 1 | BeFree |
umls:C0206708 | Cervical Intraepithelial Neoplasia | 1 | BeFree |
umls:C0279702 | Conventional (Clear Cell) Renal Cell Carcinoma | 1 | BeFree |
umls:C0302592 | Cervix carcinoma | 1 | BeFree |
umls:C0687675 | Pregnancy loss | 1 | GAD |
umls:C1847540 | Azoospermia, Nonobstructive | 1 | BeFree |
umls:C2745900 | Promyelocytic leukemia | 1 | BeFree |
umls:C0232981 | Arrest of spermatogenesis | 0 | CLINVAR,CTD_human,MGD |