TissGeneSummary for SYCP2 |
Gene summary |
Basic gene information | Gene symbol | SYCP2 |
Gene name | synaptonemal complex protein 2 | |
Synonyms | SCP2 | |
Cytomap | UCSC genome browser: 20q13.33 | |
Type of gene | protein-coding | |
RefGenes | NM_014258.2, | |
Description | SCP-2hsSCP2synaptonemal complex lateral element protein | |
Modification date | 20141207 | |
dbXrefs | MIM : 604105 | |
HGNC : HGNC | ||
Ensembl : ENSG00000196074 | ||
HPRD : 06822 | ||
Vega : OTTHUMG00000032872 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SYCP2 | |
BioGPS: 10388 | ||
Pathway | NCI Pathway Interaction Database: SYCP2 | |
KEGG: SYCP2 | ||
REACTOME: SYCP2 | ||
Pathway Commons: SYCP2 | ||
Context | iHOP: SYCP2 | |
ligand binding site mutation search in PubMed: SYCP2 | ||
UCL Cancer Institute: SYCP2 | ||
Assigned class in TissGDB* | C | |
Included tissue-specific gene expression resources | TiGER,GTEx | |
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | StomachTestis | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | STADTGCT | |
Reference showing the relevant tissue of SYCP2 | ||
Description by TissGene annotations |
* 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 SYCP2 |
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 |
KICH | 1.278762452 | -0.465381548 | 1.744144 | 3.07E-07 | 1.27E-06 |
BLCA | -0.623666601 | -2.091608706 | 1.467942105 | 0.00108 | 0.007577035 |
KIRP | -2.450758048 | -0.905845548 | -1.5449125 | 0.000422 | 0.001256473 |
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TissGene-miRNA for SYCP2 |
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 SYCP2 |
TissGeneSNV for SYCP2 |
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.S635L | UCEC | 2 |
p.S635L | BRCA | 1 |
p.E369X | COAD | 1 |
p.S1161L | OV | 1 |
p.S726L | SKCM | 1 |
p.P1182S | UCS | 1 |
p.K1427* | OV | 1 |
p.R1228W | GBM | 1 |
p.D965A | UCEC | 1 |
p.K681* | BLCA | 1 |
p.S1138L | SKCM | 1 |
p.W1083C | BLCA | 1 |
p.E1438* | SKCM | 1 |
p.C224* | UCEC | 1 |
p.D298N | UCEC | 1 |
p.S1204Y | UCEC | 1 |
p.S451T | SKCM | 1 |
p.L1435S | BLCA | 1 |
p.D937H | CESC | 1 |
p.Y1289N | HNSC | 1 |
p.P1180L | STAD | 1 |
p.D900N | UCEC | 1 |
p.F47S | SKCM | 1 |
p.E1426Q | HNSC | 1 |
p.K438E | SKCM | 1 |
p.D274N | BLCA | 1 |
p.R1181Q | BRCA | 1 |
p.P472S | COAD | 1 |
p.I1288M | STAD | 1 |
p.E1357Q | LUSC | 1 |
p.M179V | UCEC | 1 |
p.E592K | ESCA | 1 |
p.S746P | STAD | 1 |
p.R365I | COAD | 1 |
p.K669N | STAD | 1 |
p.E1210Q | HNSC | 1 |
p.T751I | COAD | 1 |
p.P429L | SKCM | 1 |
p.I744M | UCEC | 1 |
p.R1199T | BRCA | 1 |
p.E1426K | LUSC | 1 |
p.L1510F | PAAD | 1 |
p.Q847* | HNSC | 1 |
p.S529L | HNSC | 1 |
p.M271T | UCS | 1 |
p.L199I | UCEC | 1 |
p.D1004Y | OV | 1 |
p.K932T | UCEC | 1 |
p.N1024K | LUAD | 1 |
p.I646L | COAD | 1 |
p.R188Q | STAD | 1 |
p.V435I | STAD | 1 |
p.F1169I | OV | 1 |
p.M203I | LUAD | 1 |
p.G431R | SKCM | 1 |
p.Q695R | HNSC | 1 |
p.F1169L | LGG | 1 |
p.D181H | BLCA | 1 |
p.K445N | UCEC | 1 |
p.R909M | UCEC | 1 |
p.R1407_splice | UCEC | 1 |
p.W1083C | LUAD | 1 |
p.Q653H | UCEC | 1 |
p.F1414L | BRCA | 1 |
p.E1304K | BLCA | 1 |
p.K569N | BLCA | 1 |
p.E336* | UCEC | 1 |
p.W1083S | LUAD | 1 |
p.S443P | HNSC | 1 |
p.P1345H | READ | 1 |
p.E61K | ESCA | 1 |
p.K474N | HNSC | 1 |
p.K144* | SKCM | 1 |
p.S1138L | LIHC | 1 |
p.S1403N | ESCA | 1 |
p.T1386M | SKCM | 1 |
p.G95* | SKCM | 1 |
p.F858V | STAD | 1 |
p.D748Y | UCEC | 1 |
p.K108E | LUSC | 1 |
p.D209Y | UCEC | 1 |
p.R1287I | COAD | 1 |
p.T651A | LIHC | 1 |
p.K1167N | UCEC | 1 |
p.R1287I | UCEC | 1 |
p.R822I | UCEC | 1 |
p.Q1393L | LUAD | 1 |
p.D1434Y | BLCA | 1 |
p.E11X | LIHC | 1 |
p.I1408S | SKCM | 1 |
p.D922Y | UCEC | 1 |
p.R1287T | PAAD | 1 |
p.G95E | SKCM | 1 |
p.E1492X | COAD | 1 |
p.S1145* | HNSC | 1 |
p.E1038* | UCEC | 1 |
p.S1331F | SKCM | 1 |
p.Q696X | LIHC | 1 |
p.S377L | SKCM | 1 |
p.E292G | LIHC | 1 |
p.K769T | STAD | 1 |
p.R1514C | BLCA | 1 |
p.A376T | PRAD | 1 |
p.E303* | LUAD | 1 |
p.S363R | UCEC | 1 |
p.E1032K | ACC | 1 |
p.H548Y | SARC | 1 |
p.E195A | SKCM | 1 |
p.A376T | PAAD | 1 |
p.R1057I | UCEC | 1 |
p.E1113* | UCEC | 1 |
p.F388C | READ | 1 |
p.S107P | UCEC | 1 |
p.E1516* | UCEC | 1 |
p.R1365W | LUAD | 1 |
p.Q527* | BRCA | 1 |
p.I1320N | UCEC | 1 |
p.P296S | LGG | 1 |
p.E369* | STAD | 1 |
p.V1276I | THYM | 1 |
p.K1020N | STAD | 1 |
p.H237Y | LIHC | 1 |
p.R251I | CESC | 1 |
p.P450S | SKCM | 1 |
p.S579T | LIHC | 1 |
p.S783L | BLCA | 1 |
p.I733V | LUAD | 1 |
p.S635L | SKCM | 1 |
p.E796D | UCEC | 1 |
p.E171D | UCEC | 1 |
p.E344V | BLCA | 1 |
p.M1302I | ESCA | 1 |
p.Y213F | LUAD | 1 |
p.Q294K | ESCA | 1 |
p.D946Y | COAD | 1 |
p.E369X | STAD | 1 |
p.S588P | LIHC | 1 |
p.D214E | GBM | 1 |
p.I32T | DLBC | 1 |
p.N641S | BRCA | 1 |
p.E844K | SKCM | 1 |
p.E567* | UCEC | 1 |
p.L728I | COAD | 1 |
p.R1285H | CESC | 1 |
p.Q765* | PRAD | 1 |
p.E956* | UCEC | 1 |
p.L351P | SARC | 1 |
p.L301V | UCEC | 1 |
p.Q114E | BRCA | 1 |
p.G987* | BRCA | 1 |
p.F1425V | SKCM | 1 |
p.W1083X | SKCM | 1 |
p.P1186T | THYM | 1 |
p.D922Y | COAD | 1 |
p.I1007V | UCEC | 1 |
p.H1401P | ACC | 1 |
p.Q696* | LIHC | 1 |
p.D1477N | BLCA | 1 |
p.L650F | SARC | 1 |
p.N266S | UCS | 1 |
p.G270C | UCS | 1 |
p.S1451I | LUAD | 1 |
p.Q294K | UCEC | 1 |
p.R542G | PRAD | 1 |
p.N1340H | UCEC | 1 |
p.Q765X | PRAD | 1 |
p.K1192R | BLCA | 1 |
p.W618C | LUAD | 1 |
p.E1516K | PAAD | 1 |
p.E344* | BLCA | 1 |
p.E347K | UCEC | 1 |
p.Q1128* | CESC | 1 |
p.R251I | COAD | 1 |
p.S1254X | READ | 1 |
p.L1207F | LUSC | 1 |
p.Y1241* | LUAD | 1 |
p.R1397K | PAAD | 1 |
p.S451P | THYM | 1 |
p.K614R | BLCA | 1 |
p.R56W | LUAD | 1 |
p.E771K | BLCA | 1 |
p.S1204Y | READ | 1 |
p.K669Q | PAAD | 1 |
p.E773* | UCEC | 1 |
p.S1256Y | PRAD | 1 |
p.D16N | ESCA | 1 |
p.H1325D | BLCA | 1 |
p.S1214T | UCEC | 1 |
p.W716S | READ | 1 |
p.T862N | COAD | 1 |
p.S403L | BLCA | 1 |
p.R1094G | STAD | 1 |
p.T1348I | UCEC | 1 |
p.E1032Q | CESC | 1 |
p.R154H | COAD | 1 |
p.C13R | CESC | 1 |
p.G273R | LIHC | 1 |
p.W1083* | SKCM | 1 |
p.I402L | UCEC | 1 |
p.E1423D | READ | 1 |
p.E1426X | LIHC | 1 |
p.K27N | SARC | 1 |
p.K845E | STAD | 1 |
p.Q112P | UCEC | 1 |
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TissGeneCNV for SYCP2 |
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 SYCP2 |
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 | BRCA | TCGA-A2-A0CT-01A | SYCP2-ZMYND8 | In-Frame | chr20:58467044 | chr20:45927691 |
TCGAfusionPortal | PRADA | BRCA | TCGA-A1-A0SJ-01A | ADNP-SYCP2 | In-frame | Chr20:49518554 | Chr20:58468648 |
TCGAfusionPortal | PRADA | BRCA | TCGA-A2-A0CT-01A | SYCP2-ZMYND8 | In-frame | Chr20:58467045 | Chr20:45927616 |
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TissGeneNet for SYCP2 |
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 SYCP2 |
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 SYCP2 |
TissGeneDrug for SYCP2 |
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 SYCP2 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0002395 | Alzheimer's Disease | 1 | BeFree |
umls:C0004509 | Azoospermia | 1 | GAD |
umls:C0007847 | Malignant tumor of cervix | 1 | BeFree |
umls:C0028960 | Oligospermia | 1 | GAD |
umls:C0302592 | Cervix carcinoma | 1 | BeFree |
umls:C2745900 | Promyelocytic leukemia | 1 | BeFree |