SZGR2

Summary ?

GeneID	53353
Symbol	LRP1B
Synonyms	LRP-DIT\|LRPDIT
Description	LDL receptor related protein 1B
Reference	MIM:608766\|HGNC:HGNC:6693\|Ensembl:ENSG00000168702\|HPRD:16383\|Vega:OTTHUMG00000131799
Gene type	protein-coding
Map location	2q21.2
Sherlock p-value	0.119
Fetal beta	-0.335
DMG	1 (# studies)
eGene	Putamen basal ganglia

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
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: 0.023
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.02395
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
cg02322989	2	142888598	LRP1B		-0.026	0.34	DMG:Nishioka_2013

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs10211565	2	142889154	LRP1B	ENSG00000168702.12	2.18965E-6	0.03	116	gtex_brain_putamen_basal

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:0005041	low-density lipoprotein receptor activity	IEA		-
GO:0004872	receptor activity	IEA		-
GO:0005509	calcium ion binding	IEA		-
GO:0005515	protein binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006898	receptor-mediated endocytosis	TAS		10766186
GO:0015031	protein transport	TAS		10766186
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005624	membrane fraction	IEA		-
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
DELYS THYROID CANCER DN	232	154	All SZGR 2.0 genes in this pathway
ROVERSI GLIOMA COPY NUMBER DN	54	37	All SZGR 2.0 genes in this pathway
SILIGAN BOUND BY EWS FLT1 FUSION	47	34	All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS DN	193	112	All SZGR 2.0 genes in this pathway
DING LUNG CANCER MUTATED SIGNIFICANTLY	26	22	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
ULE SPLICING VIA NOVA2	43	38	All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS DN	314	188	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
BOQUEST STEM CELL UP	260	174	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL CULTURED VS FRESH UP	425	298	All SZGR 2.0 genes in this pathway
TAYLOR METHYLATED IN ACUTE LYMPHOBLASTIC LEUKEMIA	77	52	All SZGR 2.0 genes in this pathway
DING LUNG CANCER BY MUTATION RATE	20	18	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-103/107	231	237	m8	hsa-miR-103^brain	AGCAGCAUUGUACAGGGCUAUGA
miR-103/107	231	237	m8	hsa-miR-107^brain	AGCAGCAUUGUACAGGGCUAUCA
miR-130/301	207	213	1A	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-142-5p	1711	1718	1A,m8	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-142-5p	1711	1718	1A,m8	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-15/16/195/424/497	232	238	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-155	1447	1454	1A,m8	hsa-miR-155	UUAAUGCUAAUCGUGAUAGGGG
miR-183	1524	1530	1A	hsa-miR-183	UAUGGCACUGGUAGAAUUCACUG
miR-196	1505	1512	1A,m8	hsa-miR-196a	UAGGUAGUUUCAUGUUGUUGG
miR-196	1505	1512	1A,m8	hsa-miR-196b	UAGGUAGUUUCCUGUUGUUGG
miR-200bc/429	66	73	1A,m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
				hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-214	234	240	1A	hsa-miR-214^brain	ACAGCAGGCACAGACAGGCAG
miR-330	524	531	1A,m8	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-361	1353	1359	m8	hsa-miR-361^brain	UUAUCAGAAUCUCCAGGGGUAC
miR-369-3p	68	75	1A,m8	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	69	75	m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-493-5p	1441	1447	1A	hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
miR-494	1686	1692	m8	hsa-miR-494^brain	UGAAACAUACACGGGAAACCUCUU
miR-495	258	264	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-543	1586	1592	1A	hsa-miR-543	AAACAUUCGCGGUGCACUUCU

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: LRP1B