SZGR2

Summary ?

GeneID	6857
Symbol	SYT1
Synonyms	P65\|SVP65\|SYT
Description	synaptotagmin 1
Reference	MIM:185605\|HGNC:HGNC:11509\|Ensembl:ENSG00000067715\|HPRD:01710\|Vega:OTTHUMG00000134326
Gene type	protein-coding
Map location	12cen-q21
Pascal p-value	0.003
Sherlock p-value	0.923
Fetal beta	-0.706
eGene	Myers' cis & trans
Support	CANABINOID DOPAMINE EXOCYTOSIS METABOTROPIC GLUTAMATE RECEPTOR SEROTONIN 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.human_TAP-PSD-95-CORE G2Cdb.humanNRC CompositeSet Darnell FMRP targets Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
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: 5
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0024

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs7132043	chr12	80968399	SYT1	6857		0.17		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
ACTR3	0.93	0.94
GSPT2	0.92	0.93
CCT6A	0.92	0.94
SKIV2L2	0.92	0.93
ARMCX1	0.92	0.92
SNX4	0.92	0.92
COPB1	0.92	0.91
PLAA	0.92	0.93
RAB10	0.92	0.93
MATR3	0.91	0.93

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
FXYD1	-0.73	-0.85
MT-CO2	-0.73	-0.85
AF347015.33	-0.72	-0.84
AF347015.31	-0.71	-0.83
HLA-F	-0.71	-0.79
IFI27	-0.70	-0.83
AF347015.27	-0.69	-0.81
AF347015.8	-0.69	-0.83
MT-CYB	-0.68	-0.81
AF347015.2	-0.68	-0.85

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005543	phospholipid binding	TAS		1840599
GO:0005545	phosphatidylinositol binding	TAS		11438518
GO:0005509	calcium ion binding	IEA		-
GO:0005215	transporter activity	IEA		-
GO:0048306	calcium-dependent protein binding	IEA		-
GO:0017075	syntaxin-1 binding	TAS		11438518
GO:0050750	low-density lipoprotein receptor binding	IDA		15082773
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007269	neurotransmitter secretion	TAS	neuron, axon, Synap, serotonin, Neurotransmitter, dopamine (GO term level: 8)	11438518
GO:0007268	synaptic transmission	TAS	neuron, Synap, Neurotransmitter (GO term level: 6)	1840599
GO:0005513	detection of calcium ion	TAS		11438518
GO:0006810	transport	IEA		-
GO:0051260	protein homooligomerization	TAS		11438518
GO:0017157	regulation of exocytosis	TAS		11438518
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0042734	presynaptic membrane	IEA	neuron, axon, Synap (GO term level: 5)	-
GO:0043005	neuron projection	IEA	neuron, axon, neurite, dendrite (GO term level: 5)	-
GO:0030672	synaptic vesicle membrane	IEA	Synap (GO term level: 13)	-
GO:0045202	synapse	IEA	neuron, Synap, Neurotransmitter, Glial (GO term level: 2)	-
GO:0005737	cytoplasm	IEA		-
GO:0016021	integral to membrane	IEA		-
GO:0030054	cell junction	IEA		-
GO:0031410	cytoplasmic vesicle	IEA		-
GO:0030141	secretory granule	IEA		-
GO:0030666	endocytic vesicle membrane	EXP		2446925

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
C6orf15	STG	chromosome 6 open reading frame 15	Affinity Capture-Western	BioGRID	15466855
CACNA1A	APCA \| CACNL1A4 \| CAV2.1 \| EA2 \| FHM \| HPCA \| MHP \| MHP1 \| SCA6	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	-	HPRD,BioGRID	9303303
CALM1	CALML2 \| CAMI \| DD132 \| PHKD	calmodulin 1 (phosphorylase kinase, delta)	Reconstituted Complex	BioGRID	8901523
CPLX1	CPX-I \| CPX1	complexin 1	-	HPRD	7553862
FGF1	AFGF \| ECGF \| ECGF-beta \| ECGFA \| ECGFB \| FGF-alpha \| FGFA \| GLIO703 \| HBGF1	fibroblast growth factor 1 (acidic)	-	HPRD,BioGRID	11432880
GOLM1	C9orf155 \| FLJ22634 \| FLJ23608 \| GOLPH2 \| GP73 \| PSEC0257 \| bA379P1.3	golgi membrane protein 1	Two-hybrid	BioGRID	16169070
NRXN1	DKFZp313P2036 \| FLJ35941 \| Hs.22998 \| KIAA0578	neurexin 1	-	HPRD	8901523 \|11243866
S100A13	-	S100 calcium binding protein A13	-	HPRD,BioGRID	9712836 \|11432880 \|12135982
SNAP25	FLJ23079 \| RIC-4 \| RIC4 \| SEC9 \| SNAP \| SNAP-25 \| bA416N4.2 \| dJ1068F16.2	synaptosomal-associated protein, 25kDa	-	HPRD,BioGRID	10692432
STON2	STN2 \| STNB \| STNB2	stonin 2	-	HPRD,BioGRID	11381094 \|11454741
STX1A	HPC-1 \| STX1 \| p35-1	syntaxin 1A (brain)	-	HPRD,BioGRID	9010211
STX2	EPIM \| EPM \| MGC51014 \| STX2A \| STX2B \| STX2C	syntaxin 2	Reconstituted Complex	BioGRID	10397765
STX3	STX3A	syntaxin 3	Reconstituted Complex	BioGRID	10397765
STX4	STX4A \| p35-2	syntaxin 4	Reconstituted Complex	BioGRID	10397765
SV2B	HsT19680 \| KIAA0735	synaptic vesicle glycoprotein 2B	-	HPRD,BioGRID	15466855
SV2C	MGC118874 \| MGC118875 \| MGC118876 \| MGC118877	synaptic vesicle glycoprotein 2C	Affinity Capture-Western	BioGRID	15466855
SYNCRIP	GRY-RBP \| HNRPQ1 \| NSAP1 \| RP1-3J17.2 \| dJ3J17.2 \| hnRNP-Q \| pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	-	HPRD,BioGRID	10734137
SYT4	HsT1192 \| KIAA1342	synaptotagmin IV	-	HPRD	10397765
ZDHHC17	HIP14 \| HIP3 \| HSPC294 \| HYPH \| KIAA0946	zinc finger, DHHC-type containing 17	HIP14 catalyzes palmitoylation of Synaptotagmin I. This interaction was modeled on a demonstrated interaction between human HIP14 and Synaptotagmin I from an unspecified species.	BIND	15603740

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
SIG CD40PATHWAYMAP	34	28	All SZGR 2.0 genes in this pathway
REACTOME BOTULINUM NEUROTOXICITY	19	14	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 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 NOREPINEPHRINE NEUROTRANSMITTER RELEASE CYCLE	10	10	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
PARENT MTOR SIGNALING UP	567	375	All SZGR 2.0 genes in this pathway
HOOI ST7 TARGETS UP	94	57	All SZGR 2.0 genes in this pathway
DOANE BREAST CANCER ESR1 UP	112	72	All SZGR 2.0 genes in this pathway
HORIUCHI WTAP TARGETS DN	310	188	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
PROVENZANI METASTASIS UP	194	112	All SZGR 2.0 genes in this pathway
WEI MIR34A TARGETS	148	97	All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS UP	292	168	All SZGR 2.0 genes in this pathway
RICKMAN HEAD AND NECK CANCER B	48	22	All SZGR 2.0 genes in this pathway
LEE TARGETS OF PTCH1 AND SUFU DN	83	69	All SZGR 2.0 genes in this pathway
CHESLER BRAIN HIGHEST EXPRESSION	40	29	All SZGR 2.0 genes in this pathway
ZHANG TARGETS OF EWSR1 FLI1 FUSION	88	68	All SZGR 2.0 genes in this pathway
MODY HIPPOCAMPUS POSTNATAL	63	50	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
JIANG AGING HYPOTHALAMUS DN	40	31	All SZGR 2.0 genes in this pathway
JIANG AGING CEREBRAL CORTEX DN	54	43	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 1	528	324	All SZGR 2.0 genes in this pathway
LEIN NEURON MARKERS	69	45	All SZGR 2.0 genes in this pathway
RIGGINS TAMOXIFEN RESISTANCE DN	220	147	All SZGR 2.0 genes in this pathway
WANG LSD1 TARGETS DN	39	30	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION UP	461	298	All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE DN	258	160	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE UP	97	61	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B UP	172	109	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN	701	446	All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL OPTIMAL DEBULKING	246	152	All SZGR 2.0 genes in this pathway
BASSO HAIRY CELL LEUKEMIA DN	80	66	All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP	395	249	All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 ICP WITH H3K4ME3 AND H3K27ME3	34	21	All SZGR 2.0 genes in this pathway
MIKKELSEN MEF ICP WITH H3K4ME3 AND H3K27ME3	38	34	All SZGR 2.0 genes in this pathway
MIKKELSEN ES ICP WITH H3K4ME3	718	401	All SZGR 2.0 genes in this pathway
MIKKELSEN NPC ICP WITH H3K4ME3	445	257	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP	548	370	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS LOW SERUM	100	51	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT	567	365	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
SERVITJA LIVER HNF1A TARGETS DN	157	105	All SZGR 2.0 genes in this pathway
GUO TARGETS OF IRS1 AND IRS2	98	67	All SZGR 2.0 genes in this pathway
KUMAR PATHOGEN LOAD BY MACROPHAGES	275	155	All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY	1839	928	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
let-7/98	61	67	1A	hsa-let-7a^brain	UGAGGUAGUAGGUUGUAUAGUU
				hsa-let-7b^brain	UGAGGUAGUAGGUUGUGUGGUU
				hsa-let-7c^brain	UGAGGUAGUAGGUUGUAUGGUU
				hsa-let-7d^brain	AGAGGUAGUAGGUUGCAUAGU
				hsa-let-7e^brain	UGAGGUAGGAGGUUGUAUAGU
				hsa-let-7f^brain	UGAGGUAGUAGAUUGUAUAGUU
				hsa-miR-98^brain	UGAGGUAGUAAGUUGUAUUGUU
				hsa-let-7g^SZ	UGAGGUAGUAGUUUGUACAGU
				hsa-let-7i^brain	UGAGGUAGUAGUUUGUGCUGU
miR-1/206	449	455	1A	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
				hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-128	1681	1687	m8	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
				hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
				hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
				hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-129-5p	456	462	m8	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
miR-129-5p	456	462	m8	hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-133	1602	1608	1A	hsa-miR-133a	UUGGUCCCCUUCAACCAGCUGU
miR-133	1602	1608	1A	hsa-miR-133b	UUGGUCCCCUUCAACCAGCUA
miR-135	1185	1191	1A	hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
miR-135	1185	1191	1A	hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
miR-137	216	223	1A,m8	hsa-miR-137	UAUUGCUUAAGAAUACGCGUAG
miR-146	1587	1594	1A,m8	hsa-miR-146a	UGAGAACUGAAUUCCAUGGGUU
miR-146	1587	1594	1A,m8	hsa-miR-146b^brain	UGAGAACUGAAUUCCAUAGGCU
miR-148/152	1557	1563	m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-153	1624	1630	m8	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-19	142	149	1A,m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	142	149	1A,m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-193	46	52	1A	hsa-miR-193a	AACUGGCCUACAAAGUCCCAG
miR-193	46	52	1A	hsa-miR-193b	AACUGGCCCUCAAAGUCCCGCUUU
miR-200bc/429	1126	1132	m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-218	1578	1584	1A	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-221/222	1575	1581	1A	hsa-miR-221^brain	AGCUACAUUGUCUGCUGGGUUUC
miR-221/222	1575	1581	1A	hsa-miR-222^brain	AGCUACAUCUGGCUACUGGGUCUC
miR-27	1457	1463	m8	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	1457	1463	m8	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-329	1572	1578	1A	hsa-miR-329^brain	AACACACCUGGUUAACCUCUUU
miR-34/449	1539	1545	1A	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
				hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
				hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
miR-369-3p	421	427	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	421	427	m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-381	271	277	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-382	509	516	1A,m8	hsa-miR-382^brain	GAAGUUGUUCGUGGUGGAUUCG
miR-450	456	462	1A	hsa-miR-450	UUUUUGCGAUGUGUUCCUAAUA
miR-496	385	391	1A	hsa-miR-496	AUUACAUGGCCAAUCUC

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: SYT1