Gene Page: PTPRD

Summary ?
GeneID5789
SymbolPTPRD
SynonymsHPTP|HPTPD|HPTPDELTA|PTPD|RPTPDELTA
Descriptionprotein tyrosine phosphatase, receptor type D
ReferenceMIM:601598|HGNC:HGNC:9668|Ensembl:ENSG00000153707|HPRD:03358|Vega:OTTHUMG00000021005
Gene typeprotein-coding
Map location9p23-p24.3
Sherlock p-value0.122
Fetal beta1.19
DMG2 (# studies)
eGeneMyers' cis & trans
SupportG2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS
G2Cdb.humanPSD
G2Cdb.humanPSP
CompositeSet
Darnell FMRP targets
Potential synaptic genes

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
CV:PGCnpGenome-wide Association StudyGWAS
CV:PheWASPhenome-wide association studies (PheWAS)157 SNPs associated with schizophrenia 2
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. 3
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). 3
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

Section I. Genetics and epigenetics annotation

@CV:PheWAS

SNP IDChromosomePositionAllelePFunctionGeneUp/Down Distance
rs197519798846955null1.948PTPRDnull
rs1758449998879118null1.677PTPRDnull

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
ch.9.178852F98739553PTPRD2.815E-4-0.610.039DMG:Wockner_2014
cg1443995298852055PTPRD3.21E-4-0.5990.04DMG:Wockner_2014
cg0871986998857486PTPRD1.29E-8-0.015.18E-6DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs10931362chr2153744261PTPRD57890.17trans
rs1761450chr1954818034PTPRD57890.01trans
rs9637082chr2121213235PTPRD57890trans

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 V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
GAZDA DIAMOND BLACKFAN ANEMIA PROGENITOR DN 6642All SZGR 2.0 genes in this pathway
CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 DN 391222All SZGR 2.0 genes in this pathway
DAVICIONI MOLECULAR ARMS VS ERMS UP 332228All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 3D UP 182110All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC DN 537339All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS C UP 170114All SZGR 2.0 genes in this pathway
SNIJDERS AMPLIFIED IN HEAD AND NECK TUMORS 3727All SZGR 2.0 genes in this pathway
SILIGAN BOUND BY EWS FLT1 FUSION 4734All SZGR 2.0 genes in this pathway
DAWSON METHYLATED IN LYMPHOMA TCL1 5945All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM4 261153All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN 514330All SZGR 2.0 genes in this pathway
DING LUNG CANCER MUTATED SIGNIFICANTLY 2622All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN 546351All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT OK VS DONOR UP 555346All SZGR 2.0 genes in this pathway
HADDAD T LYMPHOCYTE AND NK PROGENITOR UP 7856All SZGR 2.0 genes in this pathway
MATSUDA NATURAL KILLER DIFFERENTIATION 475313All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS EARLY PROGENITOR 532309All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR UP 240152All SZGR 2.0 genes in this pathway
LEE CALORIE RESTRICTION NEOCORTEX UP 8366All SZGR 2.0 genes in this pathway
LEE AGING CEREBELLUM DN 8666All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR DN 504323All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 18HR DN 178121All SZGR 2.0 genes in this pathway
MCCLUNG CREB1 TARGETS UP 10072All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 10HR UP 10169All SZGR 2.0 genes in this pathway
BAELDE DIABETIC NEPHROPATHY DN 434302All SZGR 2.0 genes in this pathway
FOSTER TOLERANT MACROPHAGE DN 409268All SZGR 2.0 genes in this pathway
STEARMAN LUNG CANCER EARLY VS LATE UP 12589All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS PTEN DN 353226All SZGR 2.0 genes in this pathway
CAMPS COLON CANCER COPY NUMBER UP 9245All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING 510309All SZGR 2.0 genes in this pathway
ZHENG GLIOBLASTOMA PLASTICITY UP 250168All 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 UP 425298All SZGR 2.0 genes in this pathway
MOOTHA PGC 420269All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS DN 435289All SZGR 2.0 genes in this pathway
DING LUNG CANCER BY MUTATION RATE 2018All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 15 3523All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS UP 504321All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A 898516All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP 745475All SZGR 2.0 genes in this pathway
IKEDA MIR133 TARGETS UP 4327All SZGR 2.0 genes in this pathway
PLASARI TGFB1 TARGETS 10HR DN 244157All SZGR 2.0 genes in this pathway