Gene Page: CSPG4

Summary ?
GeneID1464
SymbolCSPG4
SynonymsHMW-MAA|MCSP|MCSPG|MEL-CSPG|MSK16|NG2
Descriptionchondroitin sulfate proteoglycan 4
ReferenceMIM:601172|HGNC:HGNC:2466|Ensembl:ENSG00000173546|HPRD:03105|Vega:OTTHUMG00000142836
Gene typeprotein-coding
Map location15q24.2
Pascal p-value0.316
Sherlock p-value0.762
Fetal beta-1.069
DMG1 (# studies)
eGeneMyers' cis & trans
SupportCompositeSet

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). 2
DNM:Xu_2012Whole Exome Sequencing analysisDe novo mutations of 4 genes were identified by exome sequencing of 795 samples in this study
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
CSPG4chr1575982186GANM_001897p.407P>LmissenseSchizophreniaDNM:Xu_2012

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg273781801576005446CSPG45.04E-5-0.3390.022DMG:Wockner_2014
cg221360201575986581CSPG43.859E-40.1980.043DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs12450116chr1753333924CSPG414640.03trans
rs6586252chr2144276386CSPG414640.09trans

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:0004871signal transducer activityIEA-
GO:0005082receptor signaling protein tyrosine phosphatase signaling protein activityIDA10587647 
GO:0005515protein bindingIPI10587647 
GO:0008268receptor signaling protein tyrosine kinase signaling protein activityTAS10587647 
GO:0015078hydrogen ion transmembrane transporter activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0001525angiogenesisIEA-
GO:0007165signal transductionIEA-
GO:0007275multicellular organismal developmentIEA-
GO:0030154cell differentiationIEA-
GO:0048771tissue remodelingIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0042995cell projectionIEAaxon (GO term level: 4)-
GO:0009986cell surfaceTAS10587647 
GO:0005886plasma membraneIEA-
GO:0005887integral to plasma membraneTAS8790396 
GO:0016324apical plasma membraneIEA-
GO:0016469proton-transporting two-sector ATPase complexIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PID INTEGRIN1 PATHWAY 6644All SZGR 2.0 genes in this pathway
REACTOME CS DS DEGRADATION 129All SZGR 2.0 genes in this pathway
REACTOME CHONDROITIN SULFATE BIOSYNTHESIS 2115All SZGR 2.0 genes in this pathway
REACTOME CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM 4933All SZGR 2.0 genes in this pathway
REACTOME HEPARAN SULFATE HEPARIN HS GAG METABOLISM 5233All SZGR 2.0 genes in this pathway
REACTOME GLYCOSAMINOGLYCAN METABOLISM 11169All SZGR 2.0 genes in this pathway
REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS 2517All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF CARBOHYDRATES 247154All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA UP 783507All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 UP 380236All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS UP 214155All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 8HR UP 164122All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 12HR UP 162116All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 3 4WK UP 214144All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 4 5WK DN 196131All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 5 6WK DN 13797All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS 1174695All SZGR 2.0 genes in this pathway
LIEN BREAST CARCINOMA METAPLASTIC VS DUCTAL UP 8351All SZGR 2.0 genes in this pathway
GOUYER TATI TARGETS DN 1712All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS UP 266171All SZGR 2.0 genes in this pathway
KANG IMMORTALIZED BY TERT UP 8961All SZGR 2.0 genes in this pathway
OUYANG PROSTATE CANCER PROGRESSION DN 2116All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN LUNG UP 2110All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP 648398All SZGR 2.0 genes in this pathway
ZHENG GLIOBLASTOMA PLASTICITY DN 5839All SZGR 2.0 genes in this pathway
ROSS LEUKEMIA WITH MLL FUSIONS 7849All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 36HR UP 221150All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR UP 293203All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS UP 10878All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3 UNMETHYLATED 536296All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 1069729All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN 457302All SZGR 2.0 genes in this pathway
YAGI AML WITH 11Q23 REARRANGED 351238All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC DN 253192All SZGR 2.0 genes in this pathway
ISSAEVA MLL2 TARGETS 6235All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D 882506All SZGR 2.0 genes in this pathway
PLASARI TGFB1 TARGETS 10HR UP 199143All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP 489314All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY 1839928All SZGR 2.0 genes in this pathway
NABA ECM AFFILIATED 17189All SZGR 2.0 genes in this pathway
NABA MATRISOME ASSOCIATED 753411All SZGR 2.0 genes in this pathway
NABA MATRISOME 1028559All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-148/152956962m8hsa-miR-148aUCAGUGCACUACAGAACUUUGU
hsa-miR-152brainUCAGUGCAUGACAGAACUUGGG
hsa-miR-148bUCAGUGCAUCACAGAACUUUGU