Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	STXBP1
	Gene name	syntaxin binding protein 1
	Synonyms	MUNC18-1\|NSEC1\|P67\|RBSEC1\|UNC18
	Cytomap	UCSC genome browser: 9q34.1
	Genomic location	chr9 :130374485-130454995
	Type of gene	protein-coding
	RefGenes	NM_001032221.3, NM_003165.3,
	Ensembl id	ENSG00000136854
	Description	N-Sec1neuronal SEC1protein unc-18 homolog 1protein unc-18 homolog Asyntaxin-binding protein 1unc-18Aunc18-1
	Modification date	20141207
dbXrefs	MIM : 602926
	HGNC : HGNC
	Ensembl : ENSG00000136854
	HPRD : 04235
	Vega : OTTHUMG00000020713
Protein	UniProt: P61764 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_STXBP1
	BioGPS: 6812
	Gene Expression Atlas: ENSG00000136854
	The Human Protein Atlas: ENSG00000136854
Pathway	NCI Pathway Interaction Database: STXBP1
	KEGG: STXBP1
	REACTOME: STXBP1
	ConsensusPathDB
	Pathway Commons: STXBP1
Metabolism	MetaCyc: STXBP1
	HUMANCyc: STXBP1
Regulation	Ensembl's Regulation: ENSG00000136854
	miRBase: chr9 :130,374,485-130,454,995
	TargetScan: NM_001032221
	cisRED: ENSG00000136854
Context	iHOP: STXBP1
	cancer metabolism search in PubMed: STXBP1
	UCL Cancer Institute: STXBP1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for STXBP1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM	602926; gene. 612164; phenotype.
Orphanet	1934; Early infantile epileptic encephalopathy. 33069; Dravet syndrome.
Disease	KEGG Disease: STXBP1
	MedGen: STXBP1 (Human Medical Genetics with Condition)
	ClinVar: STXBP1
Phenotype	MGI: STXBP1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	STXBP1	chr9	130434558	130434558	ENG	chr9	130595143	130595143
ovary	STXBP1	chr9	130422099	130422119	TTC16	chr9	130485019	130485039
ovary	STXBP1	chr9	130423199	130423219	STXBP1	chr9	130431387	130431407

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 STXBP1 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
BU737515	HSPB1	19	94	7	75933537	75933612	STXBP1	89	413	9	130454104	130454428
BP250257	STXBP1	1	372	9	130453452	130453823	STXBP1	369	578	9	130435472	130438222
AI014296	REEP1	1	125	2	86441947	86442071	STXBP1	125	316	9	130453518	130453709
BI059823	SMAP2	1	497	1	40885082	40885578	STXBP1	488	569	9	130453063	130453144

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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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
chr9:130440714-130440714	p.T455M	3
chr9:130438143-130438143	p.V391I	3
chr9:130430453-130430453	p.A297T	3
chr9:130425628-130425628	p.R192W	2
chr9:130430389-130430389	p.R275R	2
chr9:130432199-130432199	p.D309Y	2
chr9:130416038-130416038	p.C44C	2
chr9:130432209-130432209	p.S312C	2
chr9:130438118-130438118	p.K382K	2
chr9:130425583-130425583	p.A177T	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	3	1	9	2				2			5	1	2	1		4	7		14
# mutation	1	3	1	9	2				2			6	1	2	1		4	6		14
nonsynonymous SNV	1	3	1	9	2				1			5		1	1		3	4		12
synonymous SNV									1			1	1	1			1	2		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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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
chr9:130438143	p.V391I,STXBP1	3
chr9:130430453	p.A297T,STXBP1	3
chr9:130416038	p.P575Q	2
chr9:130453075	p.R192W,STXBP1	2
chr9:130425628	p.C44C,STXBP1	2
chr9:130432199	p.D309Y,STXBP1	2
chr9:130428533	p.T131M,STXBP1	1
chr9:130438119	p.E369D,STXBP1	1
chr9:130423393	p.G568V	1
chr9:130444743	p.A136T,STXBP1	1

Other 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

Copy 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

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.

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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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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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


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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA36241; -.
Organism-specific databases	CTD	6812; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00126	syntaxin binding protein 1	approved; nutraceutical	Vitamin C
DB00130	syntaxin binding protein 1	approved; nutraceutical; investigational	L-Glutamine
DB00149	syntaxin binding protein 1	approved; nutraceutical	L-Leucine
DB00122	syntaxin binding protein 1	approved; nutraceutical	Choline
DB00988	syntaxin binding protein 1	approved	Dopamine

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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