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| Phenotypic Information (metabolism pathway, cancer, disease, phenome) |
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| Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG |
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| Gene Summary for SNAP25 |
| Basic gene info. | Gene symbol | SNAP25 |
| Gene name | synaptosomal-associated protein, 25kDa | |
| Synonyms | RIC-4|RIC4|SEC9|SNAP|SNAP-25|bA416N4.2|dJ1068F16.2 | |
| Cytomap | UCSC genome browser: 20p12-p11.2 | |
| Genomic location | chr20 :10199476-10288066 | |
| Type of gene | protein-coding | |
| RefGenes | NM_003081.3, NM_130811.2, | |
| Ensembl id | ENSG00000132639 | |
| Description | SUPresistance to inhibitors of cholinesterase 4 homologsuper proteinsynaptosomal-associated protein 25synaptosomal-associated protein, 25kD | |
| Modification date | 20141214 | |
| dbXrefs | MIM : 600322 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000132639 | ||
| HPRD : 02637 | ||
| Vega : OTTHUMG00000031863 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_SNAP25 | |
| BioGPS: 6616 | ||
| Gene Expression Atlas: ENSG00000132639 | ||
| The Human Protein Atlas: ENSG00000132639 | ||
| Pathway | NCI Pathway Interaction Database: SNAP25 | |
| KEGG: SNAP25 | ||
| REACTOME: SNAP25 | ||
| ConsensusPathDB | ||
| Pathway Commons: SNAP25 | ||
| Metabolism | MetaCyc: SNAP25 | |
| HUMANCyc: SNAP25 | ||
| Regulation | Ensembl's Regulation: ENSG00000132639 | |
| miRBase: chr20 :10,199,476-10,288,066 | ||
| TargetScan: NM_003081 | ||
| cisRED: ENSG00000132639 | ||
| Context | iHOP: SNAP25 | |
| cancer metabolism search in PubMed: SNAP25 | ||
| UCL Cancer Institute: SNAP25 | ||
| Assigned class in ccmGDB | C | |
| Top |
| Phenotypic Information for SNAP25(metabolism pathway, cancer, disease, phenome) |
 Cancer Description | |
| Cancer | CGAP: SNAP25 |
| Familial Cancer Database: SNAP25 | |
| * This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
| Metabolic Pathway Description | |
| REACTOME_INTEGRATION_OF_ENERGY_METABOLISM | |
| Others | |
| OMIM | |
| Orphanet | |
| Disease | KEGG Disease: SNAP25 |
| MedGen: SNAP25 (Human Medical Genetics with Condition) | |
| ClinVar: SNAP25 | |
| Phenotype | MGI: SNAP25 (International Mouse Phenotyping Consortium) |
| PhenomicDB: SNAP25 | |
| Mutations for SNAP25 |
| * Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
| Structural Variants in COSMIC: go to COSMIC mutation histogram |
| - Statistics for Tissue and Mutation type | Top |
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| - For Inter-chromosomal Variations |
| There's no inter-chromosomal structural variation. |
| - For Intra-chromosomal Variations |
| * Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
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| Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
| ovary | SNAP25 | chr20 | 10275049 | 10275069 | chr20 | 12830285 | 12830305 |
| cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
| Related fusion transcripts : go to Chitars2.0 |
| * From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SNAP25 related fusion information. |
| ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
| AV726363 | LAMA3 | 1 | 286 | 18 | 21487585 | 21489176 | SNAP25 | 287 | 615 | 20 | 10286843 | 10287173 | |
| DA524284 | RASA4 | 1 | 430 | 7 | 102246371 | 102257204 | SNAP25 | 429 | 564 | 20 | 10287139 | 10287274 | |
| AW898620 | SNAP25 | 20 | 414 | 20 | 10286966 | 10287360 | SNAP25 | 403 | 620 | 20 | 10287483 | 10287698 | |
| BQ340310 | SNAP25 | 1 | 301 | 20 | 10287519 | 10287819 | IGSF9B | 297 | 392 | 11 | 133802427 | 133802522 | |
| BI033650 | SNAP25 | 2 | 178 | 20 | 10287792 | 10287974 | CREBBP | 167 | 398 | 16 | 3784039 | 3784271 | |
| AW899942 | ROR1 | 11 | 100 | 1 | 64285940 | 64286029 | SNAP25 | 93 | 383 | 20 | 10287562 | 10287852 | |
| AW900408 | SNAP25 | 10 | 222 | 20 | 10287795 | 10288007 | EHMT1 | 217 | 392 | 9 | 140514186 | 140514361 | |
| BG715348 | SNRPN | 4 | 245 | 15 | 25219969 | 25220210 | SNAP25 | 239 | 730 | 20 | 10286958 | 10287449 | |
| CD250904 | SNAP25 | 1 | 93 | 20 | 10287694 | 10287786 | SNAP25 | 84 | 577 | 20 | 10279945 | 10287152 | |
| Other DBs for Structural Variants |
| Top |
| Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
| Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
| Total # sample | 2 | 1 | ||||||||||||||||||
| GAIN (# sample) | 1 | |||||||||||||||||||
| LOSS (# sample) | 1 | 1 |
| cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
| Top |
| SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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: Non-synonymous mutation, 
: Synonymous mutation, Circle size denotes number of samples. |
| Top |
| Somatic Mutation Counts per Tissue in COSMIC data |
| Stat. for Non-Synonymous SNVs (# total SNVs=28) | (# total SNVs=10) |
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(# total SNVs=0) | (# total SNVs=1) |
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| Top |
| Top 10 SNVs Having the Most Samples in COSMIC data |
| * When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
| GRCh37 position | Mutation(aa) | Unique sampleID count |
| chr20:10273541-10273541 | p.R59C | 3 |
| chr20:10280034-10280034 | p.R176C | 3 |
| chr20:10279970-10279970 | p.S154R | 3 |
| chr20:10279981-10279981 | p.G158E | 2 |
| chr20:10277675-10277675 | p.A128A | 2 |
| chr20:10280021-10280021 | p.I171I | 2 |
| chr20:10258351-10258351 | p.R31C | 2 |
| chr20:10279941-10279941 | p.E145K | 2 |
| chr20:10256146-10256146 | p.E3K | 2 |
| chr20:10256162-10256162 | p.R8H | 2 |
| Top |
| SNV Counts per Each Loci in TCGA data |
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| Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
| # sample | 2 | 2 | 5 | 1 | 1 | 7 | 2 | 2 | 6 | 3 | 10 | |||||||||
| # mutation | 2 | 2 | 5 | 1 | 1 | 7 | 2 | 2 | 4 | 3 | 11 | |||||||||
| nonsynonymous SNV | 2 | 2 | 2 | 1 | 1 | 5 | 1 | 2 | 4 | 2 | 9 | |||||||||
| synonymous SNV | 3 | 2 | 1 | 1 | 2 |
| cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
| Top |
| Top 10 SNVs Having the Most Samples in TCGA data |
| * We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
| Genomic Position | Mutation(aa) | Unique sampleID count |
| chr20:10256162 | p.R8H,SNAP25 | 3 |
| chr20:10279981 | p.Q56Q | 2 |
| chr20:10279989 | p.G158E,SNAP25 | 2 |
| chr20:10280021 | p.R161S,SNAP25 | 2 |
| chr20:10280034 | p.I171I,SNAP25 | 2 |
| chr20:10273813 | p.R176C,SNAP25 | 2 |
| chr20:10273890 | p.G82E | 2 |
| chr20:10273897 | p.D58N | 1 |
| chr20:10265390 | p.A128A,SNAP25 | 1 |
| chr20:10273906 | p.R59C | 1 |
| Other DBs for Point Mutations |
| Copy Number for SNAP25 in TCGA |
| * Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
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| cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
| Top |
| Gene Expression for SNAP25 |
| Gene Expression in Cancer Cell-lines (CCLE) |
| * CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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| Differential Gene Expression in Primary Tumors (TCGA) |
| * Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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| Top |
| CNV vs Gene Expression Plot |
| * This plots show the correlation between CNV and gene expression. |
: Open all plots for all cancer types
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| Top |
| Gene-Gene Network Information |
| Co-Expressed gene's network Plot |
| * Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
: Open all plots for all cancer types
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| AP3B2,APLP1,BSN,CHRNB2,CPLX2,DISP2,AMER3, KCNC1,UNC79,LRTM2,NAPB,PHF21B,PTPRN2,RUNDC3A, SNAP25,SYN1,SYP,SYT4,TMEM145,UNC13A,XKR7 | ACBD7,PXYLP1,APLP1,BEND3,KIAA0226L,CRABP1,DCX, GPM6B,LRRC8D,NALCN,OAT,PAICS,PHLDA1,PRMT6, PTPN9,SNAP25,TMEM97,TP53,TRIM9,UCK2,XPNPEP1 | ||||
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| APLP1,PIANP,MIR7-3HG,CHGB,DLGAP3,AMER3,GDAP1L1, GPR6,JPH3,KCNH6,LOC254559,PRMT8,SCG3,SLC6A15, SNAP25,SPTBN4,SVOP,SYP,SYT4,TMEM59L,VGF | BCHE,FSTL5,GUCY1B3,LIX1,LPPR5,NRSN1,PLN, PPP2R2B,PTBP2,RERG,RND2,RTN1,SGCE,SLC5A7, SNAP25,SYT4,TAGLN3,TCEAL6,UCHL1,ZCCHC12,ZDHHC22 |
| Co-Expressed gene's Protein-protein interaction Network Plot |
| * Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
: Open all plots for all cancer types
| Top |
| Interacting Genes (from Pathway Commons) |
: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID
| Top |
| Pharmacological Information for SNAP25 |
| Cross-referenced pharmacological DB IDs from Uniprot |
| DB Category | DB Name | DB's ID and Url link |
| Drug-Gene Interaction Network |
| * Gene Centered Interaction Network. |
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| * Drug Centered Interaction Network. |
| DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
| DB00126 | synaptosomal-associated protein, 25kDa | approved; nutraceutical | Vitamin C |  |  |
| DB00130 | synaptosomal-associated protein, 25kDa | approved; nutraceutical; investigational | L-Glutamine |  |  |
| DB00149 | synaptosomal-associated protein, 25kDa | approved; nutraceutical | L-Leucine |  |  |
| DB00122 | synaptosomal-associated protein, 25kDa | approved; nutraceutical | Choline |  |  |
| DB00422 | synaptosomal-associated protein, 25kDa | approved; investigational | Methylphenidate |  |  |
| DB00988 | synaptosomal-associated protein, 25kDa | approved | Dopamine |  |  |
| Top |
| Cross referenced IDs for SNAP25 |
| * We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
: Open all cross reference information
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