SZGR2

Summary ?

GeneID	22871
Symbol	NLGN1
Synonyms	NL1
Description	neuroligin 1
Reference	MIM:600568\|HGNC:HGNC:14291\|Ensembl:ENSG00000169760\|HPRD:07195\|Vega:OTTHUMG00000157005
Gene type	protein-coding
Map location	3q26.31
Pascal p-value	2.755E-4
Sherlock p-value	0.004
Fetal beta	0.691
Support	CELL ADHESION AND TRANSSYNAPTIC SIGNALING G2Cdb.humanPSD G2Cdb.humanPSP Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGCnp	Genome-wide Association Study	GWAS
CV:PheWAS	Phenome-wide association studies (PheWAS)	157 SNPs associated with schizophrenia	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.
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: 5

Section I. Genetics and epigenetics annotation

CV:PheWAS

SNP ID	Chromosome	Position	Allele	P	Function	Gene	Up/Down Distance
rs13074924	3	174029045	null	1.615	NLGN1	null

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
NCOA7	0.95	0.90
COL4A3BP	0.94	0.92
CHM	0.94	0.91
PREPL	0.94	0.88
ARFGEF2	0.93	0.90
MAP2K4	0.93	0.88
PIK3CB	0.93	0.90
DPP8	0.93	0.87
ATRNL1	0.93	0.90
ATP6V1A	0.92	0.86

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
C1orf61	-0.50	-0.64
RAB34	-0.49	-0.55
AF347015.21	-0.48	-0.46
EFEMP2	-0.47	-0.53
PLA2G5	-0.47	-0.46
IL32	-0.47	-0.50
DBI	-0.47	-0.55
RHOC	-0.47	-0.58
GATSL3	-0.46	-0.53
ENHO	-0.46	-0.54

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0042043	neurexin binding	ISS	Synap (GO term level: 4)	-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007416	synaptogenesis	ISS	Synap (GO term level: 6)	-
GO:0016080	synaptic vesicle targeting	ISS	Synap (GO term level: 10)	-
GO:0045664	regulation of neuron differentiation	ISS	neuron, neurogenesis (GO term level: 9)	-
GO:0007155	cell adhesion	IEA		-
GO:0006605	protein targeting	ISS		-
GO:0016339	calcium-dependent cell-cell adhesion	ISS		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0045211	postsynaptic membrane	IEA	Synap, Neurotransmitter (GO term level: 5)	-
GO:0045202	synapse	ISS	neuron, Synap, Neurotransmitter, Glial (GO term level: 2)	-
GO:0005886	plasma membrane	IEA		-
GO:0005887	integral to plasma membrane	ISS		-
GO:0030054	cell junction	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG CELL ADHESION MOLECULES CAMS	134	93	All SZGR 2.0 genes in this pathway
ROVERSI GLIOMA COPY NUMBER UP	100	75	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 12HR UP	116	79	All SZGR 2.0 genes in this pathway
KAAB HEART ATRIUM VS VENTRICLE DN	261	183	All SZGR 2.0 genes in this pathway
BHATI G2M ARREST BY 2METHOXYESTRADIOL DN	127	75	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	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-15/16/195/424/497	645	651	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-190	120	127	1A,m8	hsa-miR-190	UGAUAUGUUUGAUAUAUUAGGU
miR-193	508	514	1A	hsa-miR-193a	AACUGGCCUACAAAGUCCCAG
miR-193	508	514	1A	hsa-miR-193b	AACUGGCCCUCAAAGUCCCGCUUU
miR-217	37	43	1A	hsa-miR-217	UACUGCAUCAGGAACUGAUUGGAU
miR-30-5p	1120	1126	m8	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-369-3p	1640	1646	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	1640	1646	m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-381	1654	1660	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-381	1654	1660	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-448	354	360	m8	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-493-5p	1399	1405	m8	hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
miR-495	971	977	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU

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: NLGN1