Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for SNAP25
Basic gene info.Gene symbolSNAP25
Gene namesynaptosomal-associated protein, 25kDa
SynonymsRIC-4|RIC4|SEC9|SNAP|SNAP-25|bA416N4.2|dJ1068F16.2
CytomapUCSC genome browser: 20p12-p11.2
Genomic locationchr20 :10199476-10288066
Type of geneprotein-coding
RefGenesNM_003081.3,
NM_130811.2,
Ensembl idENSG00000132639
DescriptionSUPresistance to inhibitors of cholinesterase 4 homologsuper proteinsynaptosomal-associated protein 25synaptosomal-associated protein, 25kD
Modification date20141214
dbXrefs MIM : 600322
HGNC : HGNC
Ensembl : ENSG00000132639
HPRD : 02637
Vega : OTTHUMG00000031863
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SNAP25
BioGPS: 6616
Gene Expression Atlas: ENSG00000132639
The Human Protein Atlas: ENSG00000132639
PathwayNCI Pathway Interaction Database: SNAP25
KEGG: SNAP25
REACTOME: SNAP25
ConsensusPathDB
Pathway Commons: SNAP25
MetabolismMetaCyc: SNAP25
HUMANCyc: SNAP25
RegulationEnsembl's Regulation: ENSG00000132639
miRBase: chr20 :10,199,476-10,288,066
TargetScan: NM_003081
cisRED: ENSG00000132639
ContextiHOP: SNAP25
cancer metabolism search in PubMed: SNAP25
UCL Cancer Institute: SNAP25
Assigned class in ccmGDBC

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Phenotypic Information for SNAP25(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SNAP25
Familial Cancer Database: SNAP25
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SNAP25
MedGen: SNAP25 (Human Medical Genetics with Condition)
ClinVar: SNAP25
PhenotypeMGI: 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovarySNAP25chr201027504910275069chr201283028512830305
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SNAP25 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AV726363LAMA31286182148758521489176SNAP25287615201028684310287173
DA524284RASA414307102246371102257204SNAP25429564201028713910287274
AW898620SNAP2520414201028696610287360SNAP25403620201028748310287698
BQ340310SNAP251301201028751910287819IGSF9B29739211133802427133802522
BI033650SNAP252178201028779210287974CREBBP1673981637840393784271
AW899942ROR11110016428594064286029SNAP2593383201028756210287852
AW900408SNAP2510222201028779510288007EHMT12173929140514186140514361
BG715348SNRPN4245152521996925220210SNAP25239730201028695810287449
CD250904SNAP25193201028769410287786SNAP2584577201027994510287152

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2         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)

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=28)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr20:10279970-10279970p.S154R3
chr20:10273541-10273541p.R59C3
chr20:10280034-10280034p.R176C3
chr20:10256162-10256162p.R8H2
chr20:10279981-10279981p.G158E2
chr20:10277675-10277675p.A128A2
chr20:10280021-10280021p.I171I2
chr20:10258351-10258351p.R31C2
chr20:10256146-10256146p.E3K2
chr20:10279941-10279941p.E145K2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22 5  1 1  72  263 10
# mutation22 5  1 1  72  243 11
nonsynonymous SNV22 2  1 1  51  242 9
synonymous SNV   3       21    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])

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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr20:10256162p.R8H,SNAP253
chr20:10273890p.Q56Q2
chr20:10279981p.G158E,SNAP252
chr20:10279989p.R161S,SNAP252
chr20:10280021p.I171I,SNAP252
chr20:10280034p.R176C,SNAP252
chr20:10273813p.G82E2
chr20:10277684p.S25L,SNAP251
chr20:10258334p.G111A,SNAP251
chr20:10286827p.K201N,SNAP251

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy 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.
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]

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Gene Expression for SNAP25

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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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Gene-Gene Network Information
check002.gifCo-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

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

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
check002.gifCo-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

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for SNAP25
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00126synaptosomal-associated protein, 25kDaapproved; nutraceuticalVitamin C
DB00130synaptosomal-associated protein, 25kDaapproved; nutraceutical; investigationalL-Glutamine
DB00149synaptosomal-associated protein, 25kDaapproved; nutraceuticalL-Leucine
DB00122synaptosomal-associated protein, 25kDaapproved; nutraceuticalCholine
DB00422synaptosomal-associated protein, 25kDaapproved; investigationalMethylphenidate
DB00988synaptosomal-associated protein, 25kDaapprovedDopamine


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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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