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| TissGeneSummary for SYP |
 Gene summary |
| Basic gene information | Gene symbol | SYP |
| Gene name | synaptophysin | |
| Synonyms | MRX96|MRXSYP | |
| Cytomap | UCSC genome browser: Xp11.23-p11.22 | |
| Type of gene | protein-coding | |
| RefGenes | NM_003179.2, | |
| Description | major synaptic vesicle protein P38 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 313475 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000102003 | ||
| HPRD : 02435 | ||
| Vega : OTTHUMG00000034557 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_SYP | |
| BioGPS: 6855 | ||
| Pathway | NCI Pathway Interaction Database: SYP | |
| KEGG: SYP | ||
| REACTOME: SYP | ||
| Pathway Commons: SYP | ||
| Context | iHOP: SYP | |
| ligand binding site mutation search in PubMed: SYP | ||
| UCL Cancer Institute: SYP | ||
| Assigned class in TissGDB* | C | |
| Included tissue-specific gene expression resources | HPA,TiGER | |
| Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | BrainEye | |
| Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | GBM,LGGUVM | |
| Reference showing the relevant tissue of SYP | ||
| Description by TissGene annotations | Protective TissGene in OS Protective TissGene in RFS | |
| * 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 SYP |
| 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) |
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| 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) |
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| 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. |
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| 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) |
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| - 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 |
| KIRC | -1.62953169 | 0.572554421 | -2.202086111 | 1.69E-42 | 8.42E-41 |
| KICH | -0.567397245 | 0.913746755 | -1.481144 | 1.77E-07 | 7.76E-07 |
| THCA | -1.689633856 | -0.240211822 | -1.449422034 | 1.37E-19 | 4.81E-18 |
| LUSC | -1.401817638 | 0.490221578 | -1.892039216 | 5.42E-16 | 3.84E-15 |
| LUAD | -1.16788897 | 0.653779996 | -1.821668966 | 1.87E-13 | 1.58E-12 |
| KIRP | -2.22107162 | 0.67143463 | -2.89250625 | 1.85E-22 | 1.48E-20 |
| COAD | -0.975583399 | 1.153016601 | -2.1286 | 5.54E-12 | 1.23E-10 |
| STAD | -0.965918495 | 0.15137213 | -1.117290625 | 0.00562 | 0.02138643 |
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| TissGene-miRNA for SYP |
| 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 SYP |
| TissGeneSNV for SYP |
| 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. |
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| 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) |
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| - nsSNVs sorted by frequency. |
| AAchange | Cancer type | # samples |
| p.D195Y | UCEC | 1 |
| p.A111V | STAD | 1 |
| p.R88Q | BLCA | 1 |
| p.F71L | ESCA | 1 |
| p.V222M | GBM | 1 |
| p.V55G | SKCM | 1 |
| p.G45S | UCEC | 1 |
| p.D83N | BLCA | 1 |
| p.A305T | LUAD | 1 |
| p.E62K | SKCM | 1 |
| p.F41L | LUAD | 1 |
| p.R184H | STAD | 1 |
| p.A161V | UCEC | 1 |
| p.Q303H | LUAD | 1 |
| p.T146M | UCEC | 1 |
| p.G16V | LUSC | 1 |
| p.G288D | UCEC | 1 |
| p.R133Q | BRCA | 1 |
| p.A37D | LUAD | 1 |
| p.Q185H | OV | 1 |
| p.A249T | LUAD | 1 |
| p.P240H | LUAD | 1 |
| p.T86S | LUAD | 1 |
| p.S158L | HNSC | 1 |
| p.G45S | OV | 1 |
| p.S101Y | PRAD | 1 |
| p.A150T | UCEC | 1 |
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| TissGeneCNV for SYP |
| 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 SYP |
| 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 | ChiTaRs | NA | BQ778546 | SYP-CPB1 | chrX:49054897 | chr3:148545668 | |
| Chimerdb3.0 | ChiTaRs | NA | BI599645 | SYP-TSPAN7 | chrX:49056649 | chrX:38525384 | |
| Chimerdb3.0 | ChiTaRs | NA | AW952111 | SYP-CYFIP2 | chrX:49045656 | chr5:156816341 | |
| Chimerdb3.0 | ChiTaRs | NA | AA317589 | SYP-CYFIP2 | chrX:49045657 | chr5:156816341 |
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| TissGeneNet for SYP |
| 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) |
| SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (tumor) | SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (normal) |
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| COAD (tumor) | COAD (normal) |
| SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (tumor) | SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (normal) |
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| HNSC (tumor) | HNSC (normal) |
| SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (tumor) | SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (normal) |
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| KICH (tumor) | KICH (normal) |
| SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (tumor) | SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (normal) |
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| KIRC (tumor) | KIRC (normal) |
| SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (tumor) | SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (normal) |
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| KIRP (tumor) | KIRP (normal) |
| SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (tumor) | SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (normal) |
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| LIHC (tumor) | LIHC (normal) |
| SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (tumor) | SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (normal) |
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| LUAD (tumor) | LUAD (normal) |
| SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (tumor) | SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (normal) |
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| LUSC (tumor) | LUSC (normal) |
| SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (tumor) | SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (normal) |
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| PRAD (tumor) | PRAD (normal) |
| SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (tumor) | SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (normal) |
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| STAD (tumor) | STAD (normal) |
| SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (tumor) | SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (normal) |
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| THCA (tumor) | THCA (normal) |
| SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (tumor) | SYP, GRB2, AP1G1, SIAH1, SIAH2, STX1A, VAMP2, EPOR (normal) |
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| TissGeneProg for SYP |
| 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. |
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| 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. |
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| 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. |
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| 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 SYP |
| TissGeneDrug for SYP |
| 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 SYP |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0036341 | Schizophrenia | 7 | BeFree,CTD_human,LHGDN |
| umls:C0002395 | Alzheimer's Disease | 5 | BeFree |
| umls:C0007095 | Carcinoid Tumor | 5 | BeFree |
| umls:C0149925 | Small cell carcinoma of lung | 5 | BeFree |
| umls:C0262584 | Carcinoma, Small Cell | 4 | BeFree |
| umls:C1263846 | Attention deficit hyperactivity disorder | 4 | BeFree,GAD |
| umls:C0027819 | Neuroblastoma | 3 | BeFree |
| umls:C0028945 | oligodendroglioma | 3 | BeFree |
| umls:C0085648 | Synovial Cyst | 3 | BeFree |
| umls:C0206754 | Neuroendocrine Tumors | 3 | BeFree |
| umls:C0338656 | Impaired cognition | 3 | BeFree |
| umls:C0751396 | Well Differentiated Oligodendroglioma | 3 | BeFree |
| umls:C1258666 | Myxoid cyst | 3 | BeFree |
| umls:C0001418 | Adenocarcinoma | 2 | BeFree,LHGDN |
| umls:C0007131 | Non-Small Cell Lung Carcinoma | 2 | BeFree,CTD_human |
| umls:C0019693 | HIV Infections | 2 | BeFree |
| umls:C0025149 | Medulloblastoma | 2 | BeFree |
| umls:C0027627 | Neoplasm Metastasis | 2 | BeFree |
| umls:C0031511 | Pheochromocytoma | 2 | BeFree |
| umls:C0031941 | Pineal Gland Neoplasm | 2 | BeFree |
| umls:C0085400 | Neurofibrillary degeneration (morphologic abnormality) | 2 | BeFree |
| umls:C0206719 | Central Neurocytoma | 2 | BeFree |
| umls:C0334299 | Carcinoid tumor no ICD-O subtype | 2 | BeFree |
| umls:C0376358 | Malignant neoplasm of prostate | 2 | BeFree |
| umls:C0600139 | Prostate carcinoma | 2 | BeFree |
| umls:C0678222 | Breast Carcinoma | 2 | BeFree |
| umls:C0700095 | Central neuroblastoma | 2 | BeFree |
| umls:C1622510 | Neurocytoma | 2 | BeFree |
| umls:C0001430 | Adenoma | 1 | BeFree |
| umls:C0001624 | Adrenal Gland Neoplasms | 1 | BeFree |
| umls:C0002736 | Amyotrophic Lateral Sclerosis | 1 | BeFree |
| umls:C0004135 | Ataxia Telangiectasia | 1 | BeFree |
| umls:C0005586 | Bipolar Disorder | 1 | BeFree |
| umls:C0006142 | Malignant neoplasm of breast | 1 | BeFree |
| umls:C0007137 | Squamous cell carcinoma | 1 | LHGDN |
| umls:C0007785 | Cerebral Infarction | 1 | BeFree |
| umls:C0009402 | Colorectal Carcinoma | 1 | BeFree |
| umls:C0011265 | Presenile dementia | 1 | BeFree |
| umls:C0011570 | Mental Depression | 1 | BeFree |
| umls:C0011581 | Depressive disorder | 1 | BeFree |
| umls:C0011847 | Diabetes | 1 | BeFree |
| umls:C0011849 | Diabetes Mellitus | 1 | BeFree |
| umls:C0013080 | Down Syndrome | 1 | BeFree |
| umls:C0014474 | Ependymoma | 1 | BeFree |
| umls:C0017075 | Ganglioneuroma | 1 | BeFree |
| umls:C0017636 | Glioblastoma | 1 | BeFree |
| umls:C0023186 | Learning Disorders | 1 | CTD_human |
| umls:C0025261 | Memory Disorders | 1 | CTD_human |
| umls:C0026277 | Mixed Salivary Gland Tumor | 1 | BeFree |
| umls:C0030421 | Paraganglioma | 1 | BeFree |
| umls:C0032000 | Pituitary Adenoma | 1 | BeFree |
| umls:C0038454 | Cerebrovascular accident | 1 | BeFree |
| umls:C0039101 | synovial sarcoma | 1 | BeFree |
| umls:C0043194 | Wiskott-Aldrich Syndrome | 1 | BeFree |
| umls:C0086648 | MPS III B | 1 | BeFree |
| umls:C0151514 | Atrophic condition of skin | 1 | BeFree |
| umls:C0206655 | Alveolar rhabdomyosarcoma | 1 | BeFree |
| umls:C0206667 | Adrenal Cortical Adenoma | 1 | BeFree |
| umls:C0206686 | Adrenocortical carcinoma | 1 | BeFree |
| umls:C0206695 | Carcinoma, Neuroendocrine | 1 | BeFree |
| umls:C0206716 | Ganglioglioma | 1 | BeFree |
| umls:C0206743 | Rhabdoid Tumor | 1 | BeFree |
| umls:C0235946 | Cerebral atrophy | 1 | BeFree |
| umls:C0238339 | Hereditary pancreatitis | 1 | BeFree |
| umls:C0238462 | Medullary carcinoma of thyroid | 1 | BeFree |
| umls:C0268393 | Familial Cerebral Amyloid Angiopathy | 1 | BeFree |
| umls:C0280785 | Diffuse Astrocytoma | 1 | BeFree |
| umls:C0497327 | Dementia | 1 | BeFree |
| umls:C0553580 | Ewings sarcoma | 1 | BeFree |
| umls:C0740391 | Middle Cerebral Artery Occlusion | 1 | BeFree |
| umls:C0751072 | Frontotemporal Lobar Degeneration | 1 | BeFree |
| umls:C1136249 | Mental Retardation, X-Linked | 1 | CTD_human |
| umls:C1368354 | Mixed Neoplasm | 1 | BeFree |
| umls:C1510489 | Cerebral Amyloid Angiopathy, Hereditary | 1 | BeFree |
| umls:C1511789 | Desmoplastic | 1 | BeFree |
| umls:C1527249 | Colorectal Cancer | 1 | BeFree |
| umls:C1861735 | Dementia, familial Danish | 1 | BeFree |
| umls:C1866282 | CEROID LIPOFUSCINOSIS, NEURONAL, 6 | 1 | CTD_human |
| umls:C2931673 | Ceroid lipofuscinosis, neuronal 1, infantile | 1 | CTD_human |
| umls:C2931784 | Amyloid angiopathy | 1 | BeFree |
| umls:C2985175 | Extraventricular Neurocytoma | 1 | BeFree |
| umls:C3275408 | MENTAL RETARDATION, X-LINKED 96 | 1 | CTD_human,UNIPROT |
| umls:C3536893 | Ewing Sarcoma/Peripheral Primitive Neuroectodermal Tumor | 1 | BeFree |
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