SZGR2

Summary ?

GeneID	8927
Symbol	BSN
Synonyms	ZNF231
Description	bassoon presynaptic cytomatrix protein
Reference	MIM:604020\|HGNC:HGNC:1117\|Ensembl:ENSG00000164061\|HPRD:04933\|Vega:OTTHUMG00000133750
Gene type	protein-coding
Map location	3p21.31
Pascal p-value	0.064
Sherlock p-value	0.373
Fetal beta	-1.2
DMG	1 (# studies)
Support	PROTEIN CLUSTERING G2Cdb.human_mGluR5 G2Cdb.humanNRC G2Cdb.humanPSD G2Cdb.humanPSP CompositeSet Darnell FMRP targets Ascano 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
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).	2
DNM:Awadalla_2010	Whole Exome Sequencing analysis	A survey of ~430 Mb of DNA from 401 synapse-expressed genes across all cases and 25 Mb of DNA in controls found 28 candidate DNMs.
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,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 2

Section I. Genetics and epigenetics annotation

DNM table

Gene	Chromosome	Position	Ref	Alt	Transcript	AA change	Mutation type	Sift	CG46	Trait	Study
BSN	chr3	49691984	G	C	BSN:NM_003458:exon5:c.G4995C:p.V1665V	V1665V	synonymous SNV			Schizophrenia	DNM:Awadalla_2010

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg08226300	3	49695806	BSN	2.471E-4	0.43	0.037	DMG:Wockner_2014
cg20948091	3	49608040	BSN	2.997E-4	0.243	0.04	DMG:Wockner_2014

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
SH2B2	0.75	0.69
MARCKSL1	0.74	0.64
PCGF2	0.73	0.59
ZBTB12	0.73	0.62
SH3BP2	0.73	0.71
SF3A2	0.72	0.62
FAM110A	0.72	0.55
PKN1	0.72	0.65
TRAF4	0.72	0.66
JUP	0.72	0.61

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
CCNI2	-0.60	-0.66
ITM2B	-0.59	-0.64
PLA2G4A	-0.58	-0.66
ME1	-0.58	-0.62
ANXA7	-0.58	-0.60
OMG	-0.58	-0.65
CHN1	-0.57	-0.66
CACNA1F	-0.57	-0.66
ACOT13	-0.56	-0.63
C5orf53	-0.56	-0.60

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0008270	zinc ion binding	IEA		-
GO:0046872	metal ion binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007268	synaptic transmission	TAS	neuron, Synap, Neurotransmitter (GO term level: 6)	10329005
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0019717	synaptosome	IEA	Synap, Brain (GO term level: 7)	-
GO:0045202	synapse	IEA	neuron, Synap, Neurotransmitter, Glial (GO term level: 2)	-
GO:0005856	cytoskeleton	IEA		-
GO:0005634	nucleus	TAS		9806829
GO:0005737	cytoplasm	IEA		-
GO:0030054	cell junction	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
STARK PREFRONTAL CORTEX 22Q11 DELETION UP	195	138	All SZGR 2.0 genes in this pathway
STARK HYPPOCAMPUS 22Q11 DELETION UP	53	40	All SZGR 2.0 genes in this pathway
STARK BRAIN 22Q11 DELETION	13	10	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL AND PROGENITOR	681	420	All SZGR 2.0 genes in this pathway
LEIN LOCALIZED TO PROXIMAL DENDRITES	37	26	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2	491	319	All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3	435	318	All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3	590	403	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

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-1/206	527	534	1A,m8	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-124.1	871	877	1A	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-125/351	2491	2497	m8	hsa-miR-125b^brain	UCCCUGAGACCCUAACUUGUGA
miR-125/351	2491	2497	m8	hsa-miR-125a^brain	UCCCUGAGACCCUUUAACCUGUG
miR-132/212	1387	1393	1A	hsa-miR-212^SZ	UAACAGUCUCCAGUCACGGCC
miR-132/212	1387	1393	1A	hsa-miR-132^brain	UAACAGUCUACAGCCAUGGUCG
miR-135	1160	1166	m8	hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
miR-135	1160	1166	m8	hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
miR-137	1058	1065	1A,m8	hsa-miR-137	UAUUGCUUAAGAAUACGCGUAG
miR-143	1342	1348	m8	hsa-miR-143^brain	UGAGAUGAAGCACUGUAGCUCA
miR-145	1451	1457	m8	hsa-miR-145	GUCCAGUUUUCCCAGGAAUCCCUU
miR-150	622	629	1A,m8	hsa-miR-150	UCUCCCAACCCUUGUACCAGUG
miR-153	1356	1363	1A,m8	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-19	1619	1625	m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	1619	1625	m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-218	1086	1092	1A	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-24	1950	1957	1A,m8	hsa-miR-24^SZ	UGGCUCAGUUCAGCAGGAACAG
miR-25/32/92/363/367	3911	3917	m8	hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
miR-30-5p	3897	3903	1A	hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
				hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
miR-330	486	492	1A	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-339	1037	1043	1A	hsa-miR-339	UCCCUGUCCUCCAGGAGCUCA
miR-342	3970	3976	1A	hsa-miR-342^brain	UCUCACACAGAAAUCGCACCCGUC
miR-448	1357	1363	1A	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-503	1559	1565	m8	hsa-miR-503	UAGCAGCGGGAACAGUUCUGCAG
miR-539	2487	2494	1A,m8	hsa-miR-539	GGAGAAAUUAUCCUUGGUGUGU
miR-9	131	137	1A	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: BSN