SZGR2

Summary ?

GeneID	81562
Symbol	LMAN2L
Synonyms	VIPL
Description	lectin, mannose binding 2 like
Reference	MIM:609552\|HGNC:HGNC:19263\|Ensembl:ENSG00000114988\|HPRD:17286\|Vega:OTTHUMG00000130453
Gene type	protein-coding
Map location	2q11.2
Pascal p-value	7.994E-4
Sherlock p-value	0.987
Fetal beta	0.649
DMG	1 (# studies)
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Nishioka_2013	Genome-wide DNA methylation analysis	The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls.	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.
GSMA_I	Genome scan meta-analysis	Psr: 0.0004
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg01990225	2	97406019	LMAN2L		-0.025	0.31	DMG:Nishioka_2013

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs2167919	chr2	12342524	LMAN2L	81562		0.14		trans
rs7706288	chr5	141864248	LMAN2L	81562		0.18		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.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005529	sugar binding	IEA		-
GO:0005537	mannose binding	TAS		12609988
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006457	protein folding	NAS		12609988
GO:0006888	ER to Golgi vesicle-mediated transport	TAS		12878160
GO:0015031	protein transport	IMP		12878160
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000139	Golgi membrane	IEA		-
GO:0005794	Golgi apparatus	IDA		12878160
GO:0005789	endoplasmic reticulum membrane	IDA		12609988
GO:0005783	endoplasmic reticulum	IEA		-
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	TAS		12609988
GO:0030134	ER to Golgi transport vesicle	NAS		12878160

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
TIEN INTESTINE PROBIOTICS 24HR UP	557	331	All SZGR 2.0 genes in this pathway
RICKMAN METASTASIS UP	344	180	All SZGR 2.0 genes in this pathway
TOYOTA TARGETS OF MIR34B AND MIR34C	463	262	All SZGR 2.0 genes in this pathway
LI INDUCED T TO NATURAL KILLER DN	116	83	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 ALL DISORDERS DURATION CORR DN	146	90	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-124.1	1172	1178	m8	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	1172	1178	1A	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	1172	1178	1A	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-15/16/195/424/497	1196	1202	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-34/449	1169	1175	m8	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
miR-34b	1170	1176	m8	hsa-miR-34b	UAGGCAGUGUCAUUAGCUGAUUG

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: LMAN2L