SZGR2

Summary ?

GeneID	6804
Symbol	STX1A
Synonyms	HPC-1\|P35-1\|STX1\|SYN1A
Description	syntaxin 1A
Reference	MIM:186590\|HGNC:HGNC:11433\|Ensembl:ENSG00000106089\|HPRD:01721\|Vega:OTTHUMG00000137422
Gene type	protein-coding
Map location	7q11.23
Pascal p-value	0.287
Sherlock p-value	0.956
Fetal beta	-1.607
DMG	1 (# studies)
eGene	Myers' cis & trans
Support	EXOCYTOSIS G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS G2Cdb.human_clathrin G2Cdb.human_Synaptosome G2Cdb.humanNRC CompositeSet Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CNV:YES	Copy number variation studies	Manual curation
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Wockner_2014	Genome-wide DNA methylation analysis	This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24).	1
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Association	A combined odds ratio method (Sun et al. 2008), association studies	2	Link to SZGene
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 2
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0456

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg06480942	7	73116029	STX1A	3.042E-4	0.621	0.04	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs10958896	chr9	10126894	STX1A	6804	0.1	trans
rs10958899	chr9	10128700	STX1A	6804	0.06	trans
rs10958907	chr9	10131580	STX1A	6804	0.13	trans
rs1322159	chr9	10132695	STX1A	6804	0.15	trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
CALM3	0.92	0.91
SYP	0.89	0.93
MOAP1	0.88	0.88
ATP6V1G2	0.88	0.88
SPRYD3	0.88	0.90
ARF3	0.87	0.87
TPRG1L	0.87	0.90
SULT4A1	0.86	0.91
AC073610.6	0.86	0.86
AC005277.1	0.86	0.88

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
RAB13	-0.46	-0.53
BCL7C	-0.41	-0.47
RPS20	-0.39	-0.43
GRTP1	-0.39	-0.40
C9orf46	-0.39	-0.36
HYAL2	-0.39	-0.40
GPR125	-0.39	-0.38
CLIC1	-0.38	-0.53
RPL34	-0.38	-0.42
CDC42EP4	-0.38	-0.36

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000149	SNARE binding	IEA		-
GO:0005484	SNAP receptor activity	IEA		-
GO:0005515	protein binding	IEA		-
GO:0019855	calcium channel inhibitor activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007268	synaptic transmission	IEA	neuron, Synap, Neurotransmitter (GO term level: 6)	-
GO:0006836	neurotransmitter transport	IEA	neuron, Neurotransmitter (GO term level: 5)	-
GO:0006886	intracellular protein transport	IEA		-
GO:0016192	vesicle-mediated transport	IEA		-
GO:0017156	calcium ion-dependent exocytosis	IEA		-
GO:0050796	regulation of insulin secretion	TAS		15537656
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005576	extracellular region	IEA		-
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-
GO:0005886	plasma membrane	EXP		8611567
GO:0005886	plasma membrane	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
APBA1	D9S411E \| MINT1 \| X11 \| X11A \| X11ALPHA	amyloid beta (A4) precursor protein-binding, family A, member 1	-	HPRD	9395480
ATP6V1B1	ATP6B1 \| MGC32642 \| RTA1B \| VATB \| VMA2 \| VPP3	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1	Reconstituted Complex	BioGRID	12651853
CACNA1D	CACH3 \| CACN4 \| CACNL1A2 \| CCHL1A2 \| Cav1.3	calcium channel, voltage-dependent, L type, alpha 1D subunit	-	HPRD	10468580
CDK5	PSSALRE	cyclin-dependent kinase 5	-	HPRD,BioGRID	9478941
CFTR	ABC35 \| ABCC7 \| CF \| CFTR/MRP \| MRP7 \| TNR-CFTR \| dJ760C5.1	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	Syntaxin 1A interacts with CFTR.	BIND	9384384 \|12446681
CFTR	ABC35 \| ABCC7 \| CF \| CFTR/MRP \| MRP7 \| TNR-CFTR \| dJ760C5.1	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	-	HPRD,BioGRID	9384384
CPLX1	CPX-I \| CPX1	complexin 1	Affinity Capture-Western Co-crystal Structure Reconstituted Complex	BioGRID	10449403 \|11832227 \|12200427
CPLX1	CPX-I \| CPX1	complexin 1	-	HPRD	7553862
CPLX2	921-L \| CPX-2 \| CPX2 \| Hfb1 \| MGC138492	complexin 2	Affinity Capture-Western	BioGRID	10449403
KCNB1	DRK1 \| KV2.1 \| h-DRK1	potassium voltage-gated channel, Shab-related subfamily, member 1	-	HPRD	12403834
KIAA1128	FLJ14262 \| FLJ25809 \| Gcap14 \| bA486O22.1	KIAA1128	Two-hybrid	BioGRID	16169070
NAPA	SNAPA	N-ethylmaleimide-sensitive factor attachment protein, alpha	Affinity Capture-Western Reconstituted Complex	BioGRID	7553862 \|7622514
NSF	SKD2	N-ethylmaleimide-sensitive factor	-	HPRD	7622514
PSEN1	AD3 \| FAD \| PS1 \| S182	presenilin 1	PS1 interacts with syntaxin 1A.	BIND	10891589
RAB27A	GS2 \| HsT18676 \| MGC117246 \| RAB27 \| RAM	RAB27A, member RAS oncogene family	-	HPRD	12101244
RNF40	BRE1B \| DKFZp686K191 \| KIAA0661 \| MGC13051 \| RBP95 \| STARING	ring finger protein 40	Affinity Capture-Western Reconstituted Complex	BioGRID	12121982
SCNN1A	ENaCa \| ENaCalpha \| FLJ21883 \| SCNEA \| SCNN1	sodium channel, nonvoltage-gated 1 alpha	Affinity Capture-Western	BioGRID	14996668
SCNN1B	ENaCb \| ENaCbeta \| SCNEB	sodium channel, nonvoltage-gated 1, beta	Affinity Capture-Western	BioGRID	14996668
SCNN1B	ENaCb \| ENaCbeta \| SCNEB	sodium channel, nonvoltage-gated 1, beta	-	HPRD	11845306
SCNN1G	ENaCg \| ENaCgamma \| PHA1 \| SCNEG	sodium channel, nonvoltage-gated 1, gamma	-	HPRD,BioGRID	14996668
SEPT2	DIFF6 \| KIAA0158 \| NEDD5 \| Pnutl3 \| hNedd5	septin 2	-	HPRD	10321247
SEPT5	CDCREL \| CDCREL-1 \| CDCREL1 \| H5 \| PNUTL1	septin 5	-	HPRD	10321247
SLC6A1	GABATHG \| GABATR \| GAT1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	-	HPRD,BioGRID	9698305 \|11017172 \|11960023
SLC6A3	DAT \| DAT1	solute carrier family 6 (neurotransmitter transporter, dopamine), member 3	DAT interacts with Syn1A.	BIND	15202772
SLC6A4	5-HTT \| 5HTT \| HTT \| OCD1 \| SERT \| hSERT	solute carrier family 6 (neurotransmitter transporter, serotonin), member 4	-	HPRD,BioGRID	12175857
SLC6A5	GLYT2 \| NET1	solute carrier family 6 (neurotransmitter transporter, glycine), member 5	Affinity Capture-Western	BioGRID	10722844
SLC6A9	DKFZp547A1118 \| GLYT1	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	-	HPRD,BioGRID	10722844
SNAP23	HsT17016 \| SNAP23A \| SNAP23B	synaptosomal-associated protein, 23kDa	-	HPRD	12209004\|12651853
SNAP23	HsT17016 \| SNAP23A \| SNAP23B	synaptosomal-associated protein, 23kDa	Affinity Capture-Western Reconstituted Complex Two-hybrid	BioGRID	8663154 \|9168999 \|9852078 \|12651853 \|12828989
SNAP25	FLJ23079 \| RIC-4 \| RIC4 \| SEC9 \| SNAP \| SNAP-25 \| bA416N4.2 \| dJ1068F16.2	synaptosomal-associated protein, 25kDa	-	HPRD	7622514 \|7768895 \|9556632 \|10373452 \|11509230\|10954418
SNAP25	FLJ23079 \| RIC-4 \| RIC4 \| SEC9 \| SNAP \| SNAP-25 \| bA416N4.2 \| dJ1068F16.2	synaptosomal-associated protein, 25kDa	-	HPRD	7622514 \|9556632\|10954418
SNAP25	FLJ23079 \| RIC-4 \| RIC4 \| SEC9 \| SNAP \| SNAP-25 \| bA416N4.2 \| dJ1068F16.2	synaptosomal-associated protein, 25kDa	Affinity Capture-Western Co-crystal Structure Reconstituted Complex Two-hybrid	BioGRID	7553862 \|7768895 \|7961655 \|8663154 \|9852078 \|10195194 \|10449403 \|10954418 \|11524423 \|11832227 \|16169070
SNAP29	CEDNIK \| FLJ21051 \| SNAP-29	synaptosomal-associated protein, 29kDa	-	HPRD,BioGRID	9852078
STX1A	HPC-1 \| STX1 \| p35-1	syntaxin 1A (brain)	Reconstituted Complex	BioGRID	10100611
STX8	CARB	syntaxin 8	-	HPRD	11101518
STXBP1	EIEE4 \| MUNC18-1 \| UNC18 \| hUNC18 \| rbSec1	syntaxin binding protein 1	Affinity Capture-Western Reconstituted Complex	BioGRID	7553862 \|7768895 \|10449403 \|12093152 \|12963086
STXBP1	EIEE4 \| MUNC18-1 \| UNC18 \| hUNC18 \| rbSec1	syntaxin binding protein 1	-	HPRD	9045631
STXBP2	Hunc18b \| MUNC18-2 \| UNC18-2 \| UNC18B \| pp10122	syntaxin binding protein 2	-	HPRD,BioGRID	7768895 \|9045631
STXBP5	FLJ30922 \| LGL3 \| LLGL3 \| MGC141942 \| MGC141968 \| Nbla04300	syntaxin binding protein 5 (tomosyn)	-	HPRD,BioGRID	9620695
STXBP6	FLJ39638 \| HSPC156 \| amisyn	syntaxin binding protein 6 (amisyn)	-	HPRD	12145319
SYP	-	synaptophysin	Affinity Capture-Western	BioGRID	7553862
SYT1	DKFZp781D2042 \| P65 \| SVP65 \| SYT	synaptotagmin I	-	HPRD,BioGRID	9010211
SYT4	HsT1192 \| KIAA1342	synaptotagmin IV	-	HPRD	10397765
SYT7	IPCA-7 \| MGC150517 \| PCANAP7 \| SYT-VII	synaptotagmin VII	-	HPRD	7791877
SYTL4	DKFZp451P0116 \| FLJ40960 \| SLP4	synaptotagmin-like 4	-	HPRD,BioGRID	12101244
TRDMT1	DNMT2 \| M.HsaIIP \| PuMet \| RNMT1	tRNA aspartic acid methyltransferase 1	Two-hybrid	BioGRID	16169070
TXLNA	DKFZp451J0118 \| IL14 \| MGC118870 \| MGC118871 \| RP4-622L5.4 \| TXLN	taxilin alpha	Reconstituted Complex	BioGRID	12558796
TXLNB	C6orf198 \| DKFZp451A175 \| LST001 \| MDP77 \| dJ522B19.2	taxilin beta	-	HPRD,BioGRID	15184072
UNC13B	MGC133279 \| MGC133280 \| MUNC13 \| UNC13 \| Unc13h2 \| hmunc13	unc-13 homolog B (C. elegans)	-	HPRD,BioGRID	8999968
VAMP1	DKFZp686H12131 \| SYB1 \| VAMP-1	vesicle-associated membrane protein 1 (synaptobrevin 1)	Two-hybrid	BioGRID	12093152
VAMP2	FLJ11460 \| SYB2 \| VAMP-2	vesicle-associated membrane protein 2 (synaptobrevin 2)	Affinity Capture-Western Co-crystal Structure Far Western Reconstituted Complex Two-hybrid	BioGRID	7553862 \|9030619 \|10100611 \|10449403 \|11832227 \|12093152
VAMP7	SYBL1 \| TI-VAMP \| VAMP-7	vesicle-associated membrane protein 7	-	HPRD,BioGRID	12853575
VAMP8	EDB	vesicle-associated membrane protein 8 (endobrevin)	-	HPRD,BioGRID	11112705
VAPB	ALS8 \| VAMP-B \| VAMP-C \| VAP-B \| VAP-C	VAMP (vesicle-associated membrane protein)-associated protein B and C	Reconstituted Complex	BioGRID	12651853
VIM	FLJ36605	vimentin	Two-hybrid	BioGRID	16169070
VPS11	END1 \| PEP5 \| RNF108 \| hVPS11	vacuolar protein sorting 11 homolog (S. cerevisiae)	VPS11 interacts with STX1A (Syntaxin-1). This interaction was modeled on a demonstrated interaction between human VPS11 and STX1A (Syntaxin-1) from an unspecified species.	BIND	14623309
VPS18	KIAA1475 \| PEP3	vacuolar protein sorting 18 homolog (S. cerevisiae)	VPS18 interacts with STX1A (Syntaxin-1). This interaction was modeled on a demonstrated interaction between human VPS18 and STX1A (Syntaxin-1) from an unspecified species.	BIND	14623309

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT	38	25	All SZGR 2.0 genes in this pathway
REACTOME BOTULINUM NEUROTOXICITY	19	14	All SZGR 2.0 genes in this pathway
REACTOME PROTEOLYTIC CLEAVAGE OF SNARE COMPLEX PROTEINS	17	12	All SZGR 2.0 genes in this pathway
REACTOME GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE	15	13	All SZGR 2.0 genes in this pathway
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES	186	155	All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM	279	221	All SZGR 2.0 genes in this pathway
REACTOME NEUROTRANSMITTER RELEASE CYCLE	34	30	All SZGR 2.0 genes in this pathway
REACTOME INTEGRATION OF ENERGY METABOLISM	120	84	All SZGR 2.0 genes in this pathway
REACTOME DOPAMINE NEUROTRANSMITTER RELEASE CYCLE	11	11	All SZGR 2.0 genes in this pathway
REACTOME ACETYLCHOLINE NEUROTRANSMITTER RELEASE CYCLE	10	9	All SZGR 2.0 genes in this pathway
REACTOME DIABETES PATHWAYS	133	91	All SZGR 2.0 genes in this pathway
REACTOME NOREPINEPHRINE NEUROTRANSMITTER RELEASE CYCLE	10	10	All SZGR 2.0 genes in this pathway
REACTOME INSULIN SYNTHESIS AND PROCESSING	21	15	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF INSULIN SECRETION	93	65	All SZGR 2.0 genes in this pathway
REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION	17	16	All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS UP	501	327	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS UP	811	508	All SZGR 2.0 genes in this pathway
FERREIRA EWINGS SARCOMA UNSTABLE VS STABLE UP	167	92	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST UP	398	262	All SZGR 2.0 genes in this pathway
VANTVEER BREAST CANCER METASTASIS DN	121	65	All SZGR 2.0 genes in this pathway
HOEGERKORP CD44 TARGETS DIRECT UP	27	21	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
KAYO AGING MUSCLE UP	244	165	All SZGR 2.0 genes in this pathway
MCCLUNG CREB1 TARGETS UP	100	72	All SZGR 2.0 genes in this pathway
BILD HRAS ONCOGENIC SIGNATURE	261	166	All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED	1229	713	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
HOFFMANN SMALL PRE BII TO IMMATURE B LYMPHOCYTE DN	50	33	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP	756	494	All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP	682	440	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP	548	370	All SZGR 2.0 genes in this pathway
WIERENGA STAT5A TARGETS DN	213	127	All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS VIA AKT1 UP	281	183	All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family	Target position			miRNA ID	miRNA seq
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-133	421	427	m8	hsa-miR-133a	UUGGUCCCCUUCAACCAGCUGU
miR-133	421	427	m8	hsa-miR-133b	UUGGUCCCCUUCAACCAGCUA
miR-15/16/195/424/497	441	447	m8	hsa-miR-15a^brain	UAGCAGCACAUAAUGGUUUGUG
				hsa-miR-16^brain	UAGCAGCACGUAAAUAUUGGCG
				hsa-miR-15b^brain	UAGCAGCACAUCAUGGUUUACA
				hsa-miR-195^SZ	UAGCAGCACAGAAAUAUUGGC
				hsa-miR-424	CAGCAGCAAUUCAUGUUUUGAA
				hsa-miR-497	CAGCAGCACACUGUGGUUUGU
miR-200bc/429	879	885	m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-217	876	883	1A,m8	hsa-miR-217	UACUGCAUCAGGAACUGAUUGGAU
miR-29	438	444	m8	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-490	451	457	1A	hsa-miR-490	CAACCUGGAGGACUCCAUGCUG
miR-9	1127	1133	m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA

SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.

Gene Page: STX1A