Gene Page: LRP4

Summary ?
GeneID4038
SymbolLRP4
SynonymsCLSS|CMS17|LRP-4|LRP10|MEGF7|SOST2
DescriptionLDL receptor related protein 4
ReferenceMIM:604270|HGNC:HGNC:6696|Ensembl:ENSG00000134569|HPRD:18517|Vega:OTTHUMG00000166700
Gene typeprotein-coding
Map location11p11.2
Pascal p-value5.581E-5
TADA p-value0.029
Fetal beta-1.334
DMG1 (# studies)
SupportCompositeSet
Ascano FMRP targets

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 1
DNM:Fromer_2014Whole Exome Sequencing analysisThis study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
LRP4chr1146903348CTNM_002334p.907G>RmissenseSchizophreniaDNM:Fromer_2014

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg230620061146940220LRP45.085E-4-0.2090.047DMG:Wockner_2014


Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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 functionGO termEvidenceNeuro keywordsPubMed ID
GO:0004872receptor activityIEA-
GO:0005509calcium ion bindingIEA-
GO:0005509calcium ion bindingNAS-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0051124synaptic growth at neuromuscular junctionIEACholinergic, Synap (GO term level: 11)-
GO:0001822kidney developmentIEA-
GO:0001942hair follicle developmentIEA-
GO:0009954proximal/distal pattern formationIEA-
GO:0009953dorsal/ventral pattern formationIEA-
GO:0008150biological_processND-
GO:0008104protein localizationIEA-
GO:0006897endocytosisIEA-
GO:0030178negative regulation of Wnt receptor signaling pathwayIEA-
GO:0042475odontogenesis of dentine-containing toothIEA-
GO:0042733embryonic digit morphogenesisIEA-
GO:0048856anatomical structure developmentIEA-
GO:0043113receptor clusteringIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005575cellular_componentND-
GO:0016020membraneIEA-
GO:0016021integral to membraneIEA-
GO:0005886plasma membraneIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL UP 285181All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 1 DN 12686All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 2 DN 7746All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 SIGNATURE 3 DN 162116All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 12HR UP 162116All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP 443294All SZGR 2.0 genes in this pathway
CHEBOTAEV GR TARGETS DN 12073All SZGR 2.0 genes in this pathway
ROVERSI GLIOMA COPY NUMBER UP 10075All SZGR 2.0 genes in this pathway
LUI THYROID CANCER CLUSTER 1 5133All SZGR 2.0 genes in this pathway
DAIRKEE TERT TARGETS UP 380213All SZGR 2.0 genes in this pathway
KIM MYCN AMPLIFICATION TARGETS UP 9264All SZGR 2.0 genes in this pathway
RICKMAN METASTASIS UP 344180All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 12HR UP 11679All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 1 DN 163115All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
DELASERNA MYOD TARGETS UP 8951All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR UP 180125All SZGR 2.0 genes in this pathway
LU AGING BRAIN UP 262186All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN 287208All SZGR 2.0 genes in this pathway
BILD E2F3 ONCOGENIC SIGNATURE 246153All SZGR 2.0 genes in this pathway
RIGGINS TAMOXIFEN RESISTANCE UP 6644All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL OPTIMAL DEBULKING 246152All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE 721492All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN 1080713All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP 489314All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-125/351111211191A,m8hsa-miR-125bbrainUCCCUGAGACCCUAACUUGUGA
hsa-miR-125abrainUCCCUGAGACCCUUUAACCUGUG
miR-130/30118701876m8hsa-miR-130abrainCAGUGCAAUGUUAAAAGGGCAU
hsa-miR-301CAGUGCAAUAGUAUUGUCAAAGC
hsa-miR-130bbrainCAGUGCAAUGAUGAAAGGGCAU
hsa-miR-454-3pUAGUGCAAUAUUGCUUAUAGGGUUU
miR-148/152192719331Ahsa-miR-148aUCAGUGCACUACAGAACUUUGU
hsa-miR-152brainUCAGUGCAUGACAGAACUUGGG
hsa-miR-148bUCAGUGCAUCACAGAACUUUGU
miR-181188818941Ahsa-miR-181abrainAACAUUCAACGCUGUCGGUGAGU
hsa-miR-181bSZAACAUUCAUUGCUGUCGGUGGG
hsa-miR-181cbrainAACAUUCAACCUGUCGGUGAGU
hsa-miR-181dbrainAACAUUCAUUGUUGUCGGUGGGUU
miR-196169175m8hsa-miR-196aUAGGUAGUUUCAUGUUGUUGG
hsa-miR-196bUAGGUAGUUUCCUGUUGUUGG
miR-199202020261Ahsa-miR-199aCCCAGUGUUCAGACUACCUGUUC
hsa-miR-199bCCCAGUGUUUAGACUAUCUGUUC
miR-200bc/42920642070m8hsa-miR-200bUAAUACUGCCUGGUAAUGAUGAC
hsa-miR-200cUAAUACUGCCGGGUAAUGAUGG
hsa-miR-429UAAUACUGUCUGGUAAAACCGU
miR-485-5p5285351A,m8hsa-miR-485-5pAGAGGCUGGCCGUGAUGAAUUC