SZGR2

Summary ?

GeneID	3949
Symbol	LDLR
Synonyms	FH\|FHC\|LDLCQ2
Description	low density lipoprotein receptor
Reference	MIM:606945\|HGNC:HGNC:6547\|Ensembl:ENSG00000130164\|HPRD:06091\|Vega:OTTHUMG00000171935
Gene type	protein-coding
Map location	19p13.2
Pascal p-value	0.81
Sherlock p-value	0.146
Fetal beta	1.215
eGene	Myers' cis & trans
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.
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0288

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs6804316	chr3	182374457	LDLR	3949		0.14		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:0005041	low-density lipoprotein receptor activity	TAS		2777800
GO:0004888	transmembrane receptor activity	TAS		6091915
GO:0004872	receptor activity	IEA		-
GO:0030229	very-low-density lipoprotein receptor activity	IEA		-
GO:0005509	calcium ion binding	IEA		-
GO:0005319	lipid transporter activity	IEA		-
GO:0008034	lipoprotein binding	TAS		6091915
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006493	protein amino acid O-linked glycosylation	TAS		6091915
GO:0008202	steroid metabolic process	IEA		-
GO:0008203	cholesterol metabolic process	IEA		-
GO:0006629	lipid metabolic process	TAS		6299582 \|10827173
GO:0006869	lipid transport	IEA		-
GO:0006897	endocytosis	TAS		12671190
GO:0034383	low-density lipoprotein particle clearance	IMP		17142622
GO:0030301	cholesterol transport	IMP		17142622
GO:0030299	cholesterol absorption	IMP		17142622
GO:0042632	cholesterol homeostasis	IEA		-
GO:0044419	interspecies interaction between organisms	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005768	endosome	IEA		-
GO:0005905	coated pit	IEA		-
GO:0005886	plasma membrane	EXP		221835 \|8300609
GO:0005886	plasma membrane	TAS		2777800
GO:0005887	integral to plasma membrane	TAS		6327078
GO:0010008	endosome membrane	EXP		221835
GO:0030669	clathrin-coated endocytic vesicle membrane	EXP		221835

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
AP1M2	AP1-mu2 \| HSMU1B \| MU-1B \| MU1B \| mu2	adaptor-related protein complex 1, mu 2 subunit	-	HPRD,BioGRID	11157985
APOB	FLDB	apolipoprotein B (including Ag(x) antigen)	-	HPRD	12031600
APOE	AD2 \| LPG \| MGC1571 \| apoprotein	apolipoprotein E	-	HPRD	12036962
CD36	CHDS7 \| FAT \| GP3B \| GP4 \| GPIV \| PASIV \| SCARB3	CD36 molecule (thrombospondin receptor)	Reconstituted Complex	BioGRID	9555943
DAB1	-	disabled homolog 1 (Drosophila)	Reconstituted Complex Two-hybrid	BioGRID	9837937 \|10827173
DAB1	-	disabled homolog 1 (Drosophila)	-	HPRD	10380922
DAB2	DOC-2 \| DOC2 \| FLJ26626	disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)	Reconstituted Complex	BioGRID	11247302
HSPA5	BIP \| FLJ26106 \| GRP78 \| MIF2	heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa)	-	HPRD,BioGRID	10906332
LDLRAP1	ARH \| ARH1 \| ARH2 \| DKFZp586D0624 \| FHCB1 \| FHCB2 \| MGC34705	low density lipoprotein receptor adaptor protein 1	-	HPRD,BioGRID	12221107
LRPAP1	A2MRAP \| A2RAP \| HBP44 \| MGC138272 \| MRAP \| RAP	low density lipoprotein receptor-related protein associated protein 1	-	HPRD,BioGRID	7822276
PF4	CXCL4 \| MGC138298 \| SCYB4	platelet factor 4	-	HPRD,BioGRID	11986215
SNX17	KIAA0064	sorting nexin 17	-	HPRD,BioGRID	12169628

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG ENDOCYTOSIS	183	132	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS	478	302	All SZGR 2.0 genes in this pathway
REACTOME LIPID DIGESTION MOBILIZATION AND TRANSPORT	46	37	All SZGR 2.0 genes in this pathway
REACTOME LIPOPROTEIN METABOLISM	28	24	All SZGR 2.0 genes in this pathway
REACTOME CHYLOMICRON MEDIATED LIPID TRANSPORT	16	15	All SZGR 2.0 genes in this pathway
WINTER HYPOXIA UP	92	57	All SZGR 2.0 genes in this pathway
WILCOX RESPONSE TO PROGESTERONE UP	152	90	All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS UP	473	314	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP	485	293	All SZGR 2.0 genes in this pathway
PUIFFE INVASION INHIBITED BY ASCITES DN	145	91	All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA DN	663	425	All SZGR 2.0 genes in this pathway
GARGALOVIC RESPONSE TO OXIDIZED PHOSPHOLIPIDS YELLOW UP	32	25	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 1 DN	126	86	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 2 DN	77	46	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 SIGNATURE 3 DN	162	116	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE FIMA UP	544	308	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE FIMA DN	284	156	All SZGR 2.0 genes in this pathway
NAGASHIMA NRG1 SIGNALING UP	176	123	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP	722	443	All SZGR 2.0 genes in this pathway
MARKEY RB1 ACUTE LOF UP	215	137	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN	1781	1082	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN DN	770	415	All SZGR 2.0 genes in this pathway
KAN RESPONSE TO ARSENIC TRIOXIDE	123	80	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
DAUER STAT3 TARGETS UP	49	35	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN	855	609	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 COMMON DN	483	336	All SZGR 2.0 genes in this pathway
DAIRKEE TERT TARGETS UP	380	213	All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 40 HELA	42	29	All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 60 HELA	46	32	All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS DN	357	212	All SZGR 2.0 genes in this pathway
BROCKE APOPTOSIS REVERSED BY IL6	144	98	All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST DN	309	206	All SZGR 2.0 genes in this pathway
KLEIN PRIMARY EFFUSION LYMPHOMA UP	51	29	All SZGR 2.0 genes in this pathway
HASLINGER B CLL WITH 13Q14 DELETION	24	18	All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS DN	234	137	All SZGR 2.0 genes in this pathway
ABE VEGFA TARGETS 2HR	34	21	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 14HR DN	298	200	All SZGR 2.0 genes in this pathway
KANG FLUOROURACIL RESISTANCE DN	16	10	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
ZHU CMV 8 HR DN	53	40	All SZGR 2.0 genes in this pathway
ZHU CMV 24 HR DN	91	64	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 18HR UP	178	111	All SZGR 2.0 genes in this pathway
ZHU CMV ALL DN	128	93	All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN	287	208	All SZGR 2.0 genes in this pathway
JACKSON DNMT1 TARGETS DN	25	21	All SZGR 2.0 genes in this pathway
DAZARD RESPONSE TO UV NHEK DN	318	220	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 12HR UP	111	68	All SZGR 2.0 genes in this pathway
TSENG IRS1 TARGETS UP	113	71	All SZGR 2.0 genes in this pathway
WANG CISPLATIN RESPONSE AND XPC UP	202	115	All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C5	46	36	All SZGR 2.0 genes in this pathway
GENTILE UV RESPONSE CLUSTER D8	40	29	All SZGR 2.0 genes in this pathway
BILD HRAS ONCOGENIC SIGNATURE	261	166	All SZGR 2.0 genes in this pathway
LEIN MEDULLA MARKERS	81	48	All SZGR 2.0 genes in this pathway
ZHANG GATA6 TARGETS DN	64	46	All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION UP	282	183	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS UP	170	107	All SZGR 2.0 genes in this pathway
ACEVEDO NORMAL TISSUE ADJACENT TO LIVER TUMOR DN	354	216	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER DN	540	340	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN UP	439	257	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER ERBB2 UP	147	83	All SZGR 2.0 genes in this pathway
BOCHKIS FOXA2 TARGETS	425	261	All SZGR 2.0 genes in this pathway
LABBE TARGETS OF TGFB1 AND WNT3A DN	108	68	All SZGR 2.0 genes in this pathway
NAKAMURA METASTASIS MODEL DN	43	28	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS DN	366	257	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO CSF2RB AND IL4 UP	338	225	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF UP	418	282	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF VS CSF2RB AND IL4 DN	245	150	All SZGR 2.0 genes in this pathway
CHANG CORE SERUM RESPONSE DN	209	137	All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A12	317	177	All SZGR 2.0 genes in this pathway
SHAFFER IRF4 TARGETS IN MYELOMA VS MATURE B LYMPHOCYTE	101	76	All SZGR 2.0 genes in this pathway
SHAFFER IRF4 TARGETS IN PLASMA CELL VS MATURE B LYMPHOCYTE	67	51	All SZGR 2.0 genes in this pathway
SHAFFER IRF4 TARGETS IN ACTIVATED B LYMPHOCYTE	81	66	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN	457	302	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS DN	668	419	All SZGR 2.0 genes in this pathway
BOYAULT LIVER CANCER SUBCLASS G6 DN	19	13	All SZGR 2.0 genes in this pathway
COULOUARN TEMPORAL TGFB1 SIGNATURE DN	138	99	All SZGR 2.0 genes in this pathway
WOO LIVER CANCER RECURRENCE DN	80	54	All SZGR 2.0 genes in this pathway
FOURNIER ACINAR DEVELOPMENT LATE 2	277	172	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 4	15	11	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 1HR UP	61	44	All SZGR 2.0 genes in this pathway
WANG RESPONSE TO GSK3 INHIBITOR SB216763 DN	374	217	All SZGR 2.0 genes in this pathway
PANGAS TUMOR SUPPRESSION BY SMAD1 AND SMAD5 DN	157	106	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP	430	288	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE	1137	655	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN	882	538	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP	570	339	All SZGR 2.0 genes in this pathway
SCHMIDT POR TARGETS IN LIMB BUD UP	26	21	All SZGR 2.0 genes in this pathway
PEDERSEN METASTASIS BY ERBB2 ISOFORM 7	403	240	All SZGR 2.0 genes in this pathway
ROLEF GLIS3 TARGETS	37	29	All SZGR 2.0 genes in this pathway
PHONG TNF TARGETS UP	63	43	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE VIA P38 PARTIAL	160	106	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE NOT VIA P38	337	236	All SZGR 2.0 genes in this pathway
VANOEVELEN MYOGENESIS SIN3A TARGETS	220	133	All SZGR 2.0 genes in this pathway
SMIRNOV RESPONSE TO IR 6HR DN	114	69	All SZGR 2.0 genes in this pathway
ZWANG CLASS 1 TRANSIENTLY INDUCED BY EGF	516	308	All SZGR 2.0 genes in this pathway
HORTON SREBF TARGETS	25	20	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-130/301	871	877	m8	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-148/152	872	878	m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-17-5p/20/93.mr/106/519.d	815	821	m8	hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU

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: LDLR