SZGR2

Summary ?

GeneID	4036
Symbol	LRP2
Synonyms	DBS\|GP330
Description	LDL receptor related protein 2
Reference	MIM:600073\|HGNC:HGNC:6694\|Ensembl:ENSG00000081479\|HPRD:02509\|Vega:OTTHUMG00000132179
Gene type	protein-coding
Map location	2q31.1
Pascal p-value	0.273
Fetal beta	-1.022
Support	Ascano FMRP targets

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.
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
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 1.3965

Section I. Genetics and epigenetics annotation

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
RUNDC3A	0.87	0.88
HAGH	0.86	0.88
RHBDD2	0.86	0.88
PGP	0.84	0.87
FKBP8	0.84	0.88
ABHD8	0.83	0.87
NBL1	0.83	0.81
RAB26	0.83	0.81
PEF1	0.83	0.82
STUB1	0.82	0.88

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
EIF5B	-0.58	-0.68
THOC2	-0.54	-0.52
AC005921.3	-0.52	-0.74
CCAR1	-0.51	-0.48
ZNF326	-0.51	-0.51
UPF3B	-0.50	-0.53
SFRS12	-0.50	-0.48
RBM25	-0.49	-0.50
MAP4K4	-0.48	-0.46
SFRS18	-0.48	-0.63

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004872	receptor activity	IEA		-
GO:0005529	sugar binding	IEA		-
GO:0005509	calcium ion binding	IEA		-
GO:0005515	protein binding	IPI		9773776 \|14528014
GO:0017124	SH3 domain binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0030900	forebrain development	IEA	Brain (GO term level: 8)	-
GO:0006486	protein amino acid glycosylation	TAS		2786251
GO:0008283	cell proliferation	IEA		-
GO:0006766	vitamin metabolic process	IEA		-
GO:0006629	lipid metabolic process	TAS		7768901
GO:0006898	receptor-mediated endocytosis	TAS		7768901
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005794	Golgi apparatus	IEA		-
GO:0005624	membrane fraction	IEA		-
GO:0005764	lysosome	TAS		7768901
GO:0005768	endosome	IEA		-
GO:0005783	endoplasmic reticulum	IEA		-
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-
GO:0005905	coated pit	IEA		-
GO:0005903	brush border	IEA		-
GO:0016324	apical plasma membrane	IEA		-
GO:0030139	endocytic vesicle	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ALB	DKFZp779N1935 \| PRO0883 \| PRO0903 \| PRO1341	albumin	-	HPRD	8898021\|11158855
ANAPC10	APC10 \| DKFZp564L0562 \| DOC1	anaphase promoting complex subunit 10	Two-hybrid	BioGRID	10827173
ANKRA2	ANKRA	ankyrin repeat, family A (RFXANK-like), 2	-	HPRD,BioGRID	11095640
ANKS1B	AIDA \| AIDA-1 \| ANKS2 \| EB-1 \| MGC26087 \| cajalin-2	ankyrin repeat and sterile alpha motif domain containing 1B	-	HPRD,BioGRID	12508107
APBA2	D15S1518E \| HsT16821 \| LIN-10 \| MGC99508 \| MGC:14091 \| MINT2 \| X11L	amyloid beta (A4) precursor protein-binding, family A, member 2	Two-hybrid	BioGRID	10827173
APBB1	FE65 \| MGC:9072 \| RIR	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	-	HPRD	9837937
APOB	FLDB	apolipoprotein B (including Ag(x) antigen)	-	HPRD	10330424
APOE	AD2 \| LPG \| MGC1571 \| apoprotein	apolipoprotein E	-	HPRD	11421580
APOE	AD2 \| LPG \| MGC1571 \| apoprotein	apolipoprotein E	Reconstituted Complex	BioGRID	7768901
APOH	B2G1 \| BG	apolipoprotein H (beta-2-glycoprotein I)	-	HPRD,BioGRID	9727058
CLU	AAG4 \| APOJ \| CLI \| KUB1 \| MGC24903 \| SGP-2 \| SGP2 \| SP-40 \| TRPM-2 \| TRPM2	clusterin	-	HPRD,BioGRID	7768901
CUBN	FLJ90055 \| FLJ90747 \| IFCR \| MGA1 \| gp280	cubilin (intrinsic factor-cobalamin receptor)	-	HPRD	11595644\|11994745
DAB1	-	disabled homolog 1 (Drosophila)	-	HPRD,BioGRID	10827173
DAB2	DOC-2 \| DOC2 \| FLJ26626	disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)	-	HPRD,BioGRID	10769163
DLG1	DKFZp761P0818 \| DKFZp781B0426 \| DLGH1 \| SAP97 \| dJ1061C18.1.1 \| hdlg	discs, large homolog 1 (Drosophila)	-	HPRD	12713445
DLG2	DKFZp781D1854 \| DKFZp781E0954 \| FLJ37266 \| MGC131811 \| PSD-93	discs, large homolog 2, chapsyn-110 (Drosophila)	-	HPRD,BioGRID	12713445
DLG3	KIAA1232 \| MRX \| MRX90 \| NE-Dlg \| NEDLG \| SAP102	discs, large homolog 3 (neuroendocrine-dlg, Drosophila)	-	HPRD,BioGRID	12713445
DLG4	FLJ97752 \| FLJ98574 \| PSD95 \| SAP90	discs, large homolog 4 (Drosophila)	-	HPRD,BioGRID	12713445
GC	DBP \| DBP/GC \| VDBG \| VDBP	group-specific component (vitamin D binding protein)	-	HPRD,BioGRID	11717447
GIPC1	C19orf3 \| GIPC \| GLUT1CBP \| Hs.6454 \| IIP-1 \| MGC15889 \| MGC3774 \| NIP \| RGS19IP1 \| SEMCAP \| SYNECTIIN \| SYNECTIN \| TIP-2	GIPC PDZ domain containing family, member 1	-	HPRD,BioGRID	11912251
GPRASP1	GASP \| GASP1 \| KIAA0443	G protein-coupled receptor associated sorting protein 1	-	HPRD	11274227
INS	ILPR \| IRDN	insulin	-	HPRD	9773776
ITGB1BP1	DKFZp686K08158 \| ICAP-1A \| ICAP-1B \| ICAP-1alpha \| ICAP1 \| ICAP1A \| ICAP1B	integrin beta 1 binding protein 1	-	HPRD,BioGRID	10827173
LDLRAP1	ARH \| ARH1 \| ARH2 \| DKFZp586D0624 \| FHCB1 \| FHCB2 \| MGC34705	low density lipoprotein receptor adaptor protein 1	-	HPRD,BioGRID	14528014
LPA	AK38 \| APOA \| LP	lipoprotein, Lp(a)	-	HPRD,BioGRID	10073957
LPL	HDLCQ11 \| LIPD	lipoprotein lipase	-	HPRD,BioGRID	7686151
LRP2BP	DKFZp761O0113 \| FLJ44965	LRP2 binding protein	-	HPRD,BioGRID	12508107
LRPAP1	A2MRAP \| A2RAP \| HBP44 \| MGC138272 \| MRAP \| RAP	low density lipoprotein receptor-related protein associated protein 1	-	HPRD,BioGRID	7512726
MAGI1	AIP3 \| BAIAP1 \| BAP1 \| MAGI-1 \| TNRC19 \| WWP3	membrane associated guanylate kinase, WW and PDZ domain containing 1	-	HPRD,BioGRID	11274227
MAPK8IP1	IB1 \| JIP-1 \| JIP1 \| PRKM8IP	mitogen-activated protein kinase 8 interacting protein 1	-	HPRD,BioGRID	10827173
MAPK8IP2	IB2 \| JIP2 \| PRKM8IPL	mitogen-activated protein kinase 8 interacting protein 2	Reconstituted Complex Two-hybrid	BioGRID	10827173 \|12508107
MDK	FLJ27379 \| MK \| NEGF2	midkine (neurite growth-promoting factor 2)	-	HPRD	10772929
NOS1AP	6330408P19Rik \| CAPON \| MGC138500	nitric oxide synthase 1 (neuronal) adaptor protein	-	HPRD,BioGRID	10827173
PLAU	ATF \| UPA \| URK \| UROKINASE \| u-PA	plasminogen activator, urokinase	-	HPRD,BioGRID	8344937
RBP1	CRABP-I \| CRBP \| CRBP1 \| CRBPI \| RBPC	retinol binding protein 1, cellular	-	HPRD,BioGRID	10203351
SCGB1A1	CC10 \| CC16 \| CCSP \| UGB	secretoglobin, family 1A, member 1 (uteroglobin)	-	HPRD,BioGRID	11278724
SCN3A	KIAA1356 \| NAC3 \| Nav1.3	sodium channel, voltage-gated, type III, alpha subunit	Two-hybrid	BioGRID	10827173
SERPINE1	PAI \| PAI-1 \| PAI1 \| PLANH1	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	-	HPRD	8344937
SLC9A3	MGC126718 \| MGC126720 \| NHE3	solute carrier family 9 (sodium/hydrogen exchanger), member 3	-	HPRD	10364184
SNX17	KIAA0064	sorting nexin 17	Reconstituted Complex	BioGRID	12169628
SYNJ2BP	ARIP2 \| FLJ11271 \| FLJ41973 \| OMP25	synaptojanin 2 binding protein	-	HPRD,BioGRID	10827173
TG	AITD3 \| TGN	thyroglobulin	-	HPRD	9492085
THBS1	THBS \| TSP \| TSP1	thrombospondin 1	Reconstituted Complex	BioGRID	7775583
TLN1	ILWEQ \| KIAA1027 \| TLN	talin 1	-	HPRD	10827173
TTR	HsT2651 \| PALB \| TBPA	transthyretin	-	HPRD	10982792

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG HEDGEHOG SIGNALING PATHWAY	56	42	All SZGR 2.0 genes in this pathway
PID HEDGEHOG 2PATHWAY	22	17	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF STEROID HORMONES AND VITAMINS A AND D	35	23	All SZGR 2.0 genes in this pathway
REACTOME STEROID HORMONES	29	21	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS	478	302	All SZGR 2.0 genes in this pathway
GAL LEUKEMIC STEM CELL DN	244	153	All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER DN	232	154	All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS	988	594	All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS	734	436	All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS	1038	678	All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS	1062	725	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS	652	441	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN	546	351	All SZGR 2.0 genes in this pathway
BECKER TAMOXIFEN RESISTANCE DN	52	37	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT OK VS DONOR UP	555	346	All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS UP	214	133	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP	491	316	All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3	1069	729	All SZGR 2.0 genes in this pathway
LOPEZ EPITHELIOID MESOTHELIOMA	17	11	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 11	103	68	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A	898	516	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-101	1069	1076	1A,m8	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-139	560	567	1A,m8	hsa-miR-139^brain	UCUACAGUGCACGUGUCU
miR-142-5p	86	92	m8	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-144	1070	1076	1A	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-15/16/195/424/497	1441	1447	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-19	38	45	1A,m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	38	45	1A,m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-204/211	1000	1007	1A,m8	hsa-miR-204^brain	UUCCCUUUGUCAUCCUAUGCCU
miR-204/211	1000	1007	1A,m8	hsa-miR-211	UUCCCUUUGUCAUCCUUCGCCU
miR-409-3p	76	83	1A,m8	hsa-miR-409-3p	CGAAUGUUGCUCGGUGAACCCCU
miR-455	41	47	1A	hsa-miR-455	UAUGUGCCUUUGGACUACAUCG
miR-93.hd/291-3p/294/295/302/372/373/520	469	476	1A,m8	hsa-miR-93^brain	AAAGUGCUGUUCGUGCAGGUAG
				hsa-miR-302a	UAAGUGCUUCCAUGUUUUGGUGA
				hsa-miR-302b	UAAGUGCUUCCAUGUUUUAGUAG
				hsa-miR-302c	UAAGUGCUUCCAUGUUUCAGUGG
				hsa-miR-302d	UAAGUGCUUCCAUGUUUGAGUGU
				hsa-miR-372	AAAGUGCUGCGACAUUUGAGCGU
				hsa-miR-373	GAAGUGCUUCGAUUUUGGGGUGU
				hsa-miR-520e	AAAGUGCUUCCUUUUUGAGGG
				hsa-miR-520a	AAAGUGCUUCCCUUUGGACUGU
				hsa-miR-520b	AAAGUGCUUCCUUUUAGAGGG
				hsa-miR-520c	AAAGUGCUUCCUUUUAGAGGGUU
				hsa-miR-520d	AAAGUGCUUCUCUUUGGUGGGUU

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: LRP2