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 STXBP1
Basic gene info.Gene symbolSTXBP1
Gene namesyntaxin binding protein 1
SynonymsMUNC18-1|NSEC1|P67|RBSEC1|UNC18
CytomapUCSC genome browser: 9q34.1
Genomic locationchr9 :130374485-130454995
Type of geneprotein-coding
RefGenesNM_001032221.3,
NM_003165.3,
Ensembl idENSG00000136854
DescriptionN-Sec1neuronal SEC1protein unc-18 homolog 1protein unc-18 homolog Asyntaxin-binding protein 1unc-18Aunc18-1
Modification date20141207
dbXrefs MIM : 602926
HGNC : HGNC
Ensembl : ENSG00000136854
HPRD : 04235
Vega : OTTHUMG00000020713
ProteinUniProt: P61764
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_STXBP1
BioGPS: 6812
Gene Expression Atlas: ENSG00000136854
The Human Protein Atlas: ENSG00000136854
PathwayNCI Pathway Interaction Database: STXBP1
KEGG: STXBP1
REACTOME: STXBP1
ConsensusPathDB
Pathway Commons: STXBP1
MetabolismMetaCyc: STXBP1
HUMANCyc: STXBP1
RegulationEnsembl's Regulation: ENSG00000136854
miRBase: chr9 :130,374,485-130,454,995
TargetScan: NM_001032221
cisRED: ENSG00000136854
ContextiHOP: STXBP1
cancer metabolism search in PubMed: STXBP1
UCL Cancer Institute: STXBP1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for STXBP1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: STXBP1
Familial Cancer Database: STXBP1
* 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 602926; gene.
612164; phenotype.
Orphanet 1934; Early infantile epileptic encephalopathy.
33069; Dravet syndrome.
DiseaseKEGG Disease: STXBP1
MedGen: STXBP1 (Human Medical Genetics with Condition)
ClinVar: STXBP1
PhenotypeMGI: STXBP1 (International Mouse Phenotyping Consortium)
PhenomicDB: STXBP1

Mutations for STXBP1
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
breastSTXBP1chr9130434558130434558ENGchr9130595143130595143
ovarySTXBP1chr9130422099130422119TTC16chr9130485019130485039
ovarySTXBP1chr9130423199130423219STXBP1chr9130431387130431407
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 STXBP1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU737515HSPB1199477593353775933612STXBP1894139130454104130454428
BP250257STXBP113729130453452130453823STXBP13695789130435472130438222
AI014296REEP1112528644194786442071STXBP11253169130453518130453709
BI059823SMAP2149714088508240885578STXBP14885699130453063130453144

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                
GAIN (# sample)2                
LOSS (# sample)                 
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=44)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted 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
chr9:130440714-130440714p.T455M3
chr9:130438143-130438143p.V391I3
chr9:130430453-130430453p.A297T3
chr9:130432209-130432209p.S312C2
chr9:130416038-130416038p.C44C2
chr9:130438118-130438118p.K382K2
chr9:130425628-130425628p.R192W2
chr9:130430389-130430389p.R275R2
chr9:130432199-130432199p.D309Y2
chr9:130442513-130442513p.T513T1

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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
# sample13192   2  5121 47 14
# mutation13192   2  6121 46 14
nonsynonymous SNV13192   1  5 11 34 12
synonymous SNV        1  111  12 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
chr9:130438143p.A297T,STXBP13
chr9:130430453p.V391I,STXBP13
chr9:130432199p.C44C,STXBP12
chr9:130416038p.D309Y,STXBP12
chr9:130453075p.P575Q2
chr9:130425628p.R192W,STXBP12
chr9:130440725p.D238H,STXBP11
chr9:130416074p.G447G,STXBP11
chr9:130453129p.T56M,STXBP11
chr9:130427551p.A251G,STXBP11

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 STXBP1 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 STXBP1

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

ABCA2,ACTL6B,AP3B2,BSN,CAMK2N2,DISP2,DNM1,
FAM57B,UNC79,MAPK8IP1,MYT1,NRSN1,RAB39B,RALYL,
RIMKLA,RUNDC3A,SCAMP5,SCG3,STX1A,STXBP1,SYP
ACO1,ANO6,AOC3,CAT,EBF1,ESYT1,FERMT2,
GNAI1,GYG2,HRASLS5,KCNIP2,LPL,MARC1,PDE3B,
PDE8A,PEX19,PLIN1,SIK2,STXBP1,SLC35G2,TYRO3

AQP3,HID1,C2orf70,CHRM1,DPYSL2,ETV5,FAM167A,
KLHL32,MAPRE2,MIA3,NAB1,NEURL1,PIAS3,RAP1GAP,
SHF,SLAIN1,SLC27A1,SOX13,STXBP1,TBC1D8,TXNDC5
ABLIM3,ADAM33,ARMCX2,DLG4,EFS,FAM65A,FKBP10,
LARP6,LDOC1,LPHN2,MAP7D3,NFATC4,NLGN3,OLFML3,
PAM,POU6F1,PRPF40B,RIMKLB,STXBP1,TENC1,ZFPM2
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 STXBP1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA36241; -.
Organism-specific databasesCTD 6812; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00126syntaxin binding protein 1approved; nutraceuticalVitamin C
DB00130syntaxin binding protein 1approved; nutraceutical; investigationalL-Glutamine
DB00149syntaxin binding protein 1approved; nutraceuticalL-Leucine
DB00122syntaxin binding protein 1approved; nutraceuticalCholine
DB00988syntaxin binding protein 1approvedDopamine


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Cross referenced IDs for STXBP1
* 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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