Summary ?
GeneID89781
SymbolHPS4
SynonymsBLOC3S2|LE
DescriptionHPS4, biogenesis of lysosomal organelles complex 3 subunit 2
ReferenceMIM:606682|HGNC:HGNC:15844|Ensembl:ENSG00000100099|HPRD:05983|Vega:OTTHUMG00000030459
Gene typeprotein-coding
Map location22cen-q12.3
Pascal p-value0.514
Fetal beta0.572
DMG1 (# studies)
eGeneCerebellar Hemisphere
SupportAscano FMRP targets

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
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
GSMA_IGenome scan meta-analysisPsr: 0.031 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg046265742226879726HPS42.71E-8-0.0228.56E-6DMG:Jaffe_2016


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:0042803protein homodimerization activityIPI12663659 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0048075positive regulation of eye pigmentationTAS11836498 
GO:0007599hemostasisTAS11836498 
GO:0007040lysosome organizationIDA12663659 
GO:0006605protein targetingIDA12663659 
GO:0050821protein stabilizationIPI12663659 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0042827platelet dense granuleIDAserotonin (GO term level: 11)12756248 
GO:0005624membrane fractionIDA12756248 
GO:0005737cytoplasmIDA12756248 
GO:0005764lysosomeIDA12663659 
GO:0042470melanosomeIDA12663659 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PARENT MTOR SIGNALING UP 567375All SZGR 2.0 genes in this pathway
GAZDA DIAMOND BLACKFAN ANEMIA ERYTHROID DN 493298All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP 485293All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA DN 663425All SZGR 2.0 genes in this pathway
WANG CLIM2 TARGETS UP 269146All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN 362238All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE FIMA UP 544308All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LPS UP 431237All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 8HR DN 12984All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747453All SZGR 2.0 genes in this pathway
BENPORATH CYCLING GENES 648385All SZGR 2.0 genes in this pathway
NADLER HYPERGLYCEMIA AT OBESITY 5835All SZGR 2.0 genes in this pathway
HADDAD B LYMPHOCYTE PROGENITOR 293193All SZGR 2.0 genes in this pathway
MCCLUNG COCAINE REWARD 5D 7962All SZGR 2.0 genes in this pathway
KONDO PROSTATE CANCER HCP WITH H3K27ME3 9772All SZGR 2.0 genes in this pathway
AGUIRRE PANCREATIC CANCER COPY NUMBER DN 238145All SZGR 2.0 genes in this pathway
VALK AML CLUSTER 4 3117All SZGR 2.0 genes in this pathway
WHITFIELD CELL CYCLE G2 M 216124All SZGR 2.0 genes in this pathway