Gene Page: PDGFRL

Summary ?
GeneID5157
SymbolPDGFRL
SynonymsPDGRL|PRLTS
Descriptionplatelet derived growth factor receptor like
ReferenceMIM:604584|HGNC:HGNC:8805|Ensembl:ENSG00000104213|HPRD:05206|Vega:OTTHUMG00000130818
Gene typeprotein-coding
Map location8p22-p21.3
Pascal p-value0.071
Fetal beta-0.349
DMG1 (# studies)
eGeneCerebellum
Myers' cis & trans
Meta

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
GSMA_IGenome scan meta-analysisPsr: 0.031 
GSMA_IIEGenome scan meta-analysis (European-ancestry samples)Psr: 0.00057 
GSMA_IIAGenome scan meta-analysis (All samples)Psr: 0.03086 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg10501177817435088PDGFRL2.3E-8-0.0147.61E-6DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs17131472chr191962966PDGFRL51570.07trans
rs2976809chr3125451738PDGFRL51570.01trans
rs16889842chr49872012PDGFRL51570.01trans
rs12647883chr49878463PDGFRL51570.14trans
rs4033102chr4111784204PDGFRL51570.16trans
rs509952chr4111788169PDGFRL51570.16trans
rs313946chr4113975904PDGFRL51570trans
rs657141chr4113981041PDGFRL51570.12trans
rs7789950PDGFRL51570.2trans
rs17056435chr5158453782PDGFRL51570.04trans
rs6920042chr667907570PDGFRL51570.02trans
rs6455226chr667930295PDGFRL51570.17trans
rs9451867chr692659609PDGFRL51578.474E-4trans
rs10958892chr910125117PDGFRL51570.07trans
rs10958896chr910126894PDGFRL51570.08trans
rs10958899chr910128700PDGFRL51570.09trans
rs10958907chr910131580PDGFRL51570.08trans
rs10958910chr910134759PDGFRL51570.17trans
rs998410chr9117622673PDGFRL51570.05trans
rs9423711chr102574802PDGFRL51570.07trans
rs107479720PDGFRL51570.04trans
rs11112163chr12105072508PDGFRL51570.07trans
rs9551590chr1329589464PDGFRL51570trans
rs10142086chr1435135892PDGFRL51570.18trans
rs2093759chr1497171024PDGFRL51570.03trans
rs17244419chr1497171074PDGFRL51574.64E-4trans
rs7177212chr1534425413PDGFRL51570.03trans
rs13380712chr1625601181PDGFRL51570.2trans
rs16961159chr1659561686PDGFRL51570.19trans
rs17841422chr1720969134PDGFRL51570.05trans
rs16977927chr1772154232PDGFRL51570.02trans
rs7236104chr1814032818PDGFRL51570.03trans
rs11873703chr1861448702PDGFRL51570.1trans
rs6095741chr2048666589PDGFRL51571.51E-4trans

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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
MED230.920.94
TTC170.920.93
C21orf660.920.93
FIGNL10.920.93
ZC3H7A0.920.94
HARS20.910.91
ZNF2110.910.91
PALB20.910.94
CCDC820.900.92
ZNF230.900.91
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.31-0.77-0.86
MT-CO2-0.77-0.86
IFI27-0.75-0.85
AF347015.27-0.74-0.82
MT-CYB-0.74-0.83
AF347015.8-0.73-0.85
AF347015.33-0.73-0.81
HIGD1B-0.72-0.85
AIFM3-0.72-0.76
FXYD1-0.71-0.82

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005019platelet-derived growth factor beta-receptor activityTAS7898930 
GO:0004992platelet activating factor receptor activityTAS7898930 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0008150biological_processND-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005576extracellular regionIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
DAVICIONI MOLECULAR ARMS VS ERMS DN 182111All SZGR 2.0 genes in this pathway
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS DN 463290All SZGR 2.0 genes in this pathway
CORRE MULTIPLE MYELOMA UP 7445All SZGR 2.0 genes in this pathway
SENESE HDAC1 AND HDAC2 TARGETS DN 232139All SZGR 2.0 genes in this pathway
ELVIDGE HYPOXIA UP 171112All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN 1375806All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN 781465All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 1 DN 378231All SZGR 2.0 genes in this pathway
CHIN BREAST CANCER COPY NUMBER DN 1610All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN DN 172112All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS E UP 9760All SZGR 2.0 genes in this pathway
HAMAI APOPTOSIS VIA TRAIL UP 584356All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 2B 392251All SZGR 2.0 genes in this pathway
DACOSTA ERCC3 ALLELE XPCS VS TTD DN 3627All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 UP 256159All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS UP 266171All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR DN 504323All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE BY 4NQO 3824All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE DN 195135All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS UP 317208All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION UP 461298All SZGR 2.0 genes in this pathway
AMBROSINI FLAVOPIRIDOL TREATMENT TP53 10963All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL UP 260174All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL CULTURED VS FRESH DN 3125All SZGR 2.0 genes in this pathway
CLIMENT BREAST CANCER COPY NUMBER DN 87All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS DN 442275All SZGR 2.0 genes in this pathway
CHEN METABOLIC SYNDROM NETWORK 1210725All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP 605377All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT 567365All SZGR 2.0 genes in this pathway
KIM GLIS2 TARGETS UP 8461All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D 882506All SZGR 2.0 genes in this pathway