Gene Page: RAPGEF1

Summary ?
GeneID2889
SymbolRAPGEF1
SynonymsC3G|GRF2
DescriptionRap guanine nucleotide exchange factor 1
ReferenceMIM:600303|HGNC:HGNC:4568|Ensembl:ENSG00000107263|HPRD:02627|Vega:OTTHUMG00000020829
Gene typeprotein-coding
Map location9q34.3
Pascal p-value0.57
Sherlock p-value0.45
Fetal beta1.056
DMG2 (# studies)
eGeneCerebellar Hemisphere
Myers' cis & trans
SupportCompositeSet
Darnell FMRP targets

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
CV:PGCnpGenome-wide Association StudyGWAS
DMG:vanEijk_2014Genome-wide DNA methylation analysisThis dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250). 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

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg136552509134544528RAPGEF13.093E-40.6150.04DMG:Wockner_2014
cg270249229134378058RAPGEF19.58E-65.148DMG:vanEijk_2014
cg259543549133971548RAPGEF19.282E-44.479DMG:vanEijk_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs12353112chr9133765871RAPGEF128890.17cis
rs1420486chr8132660693RAPGEF128890.19trans

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
PITPNM10.820.81
CHRNA40.800.79
DNER0.800.84
PLA2G150.790.80
SYT30.780.84
WNT40.770.70
PIP5KL10.760.78
RGS190.760.77
KCND20.760.76
WNT30.750.77
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
COPZ2-0.41-0.56
AF347015.31-0.41-0.58
AC021016.1-0.40-0.59
AF347015.33-0.40-0.54
MT-CO2-0.40-0.58
COX4I2-0.39-0.53
AF347015.27-0.39-0.54
AF347015.2-0.39-0.55
AF347015.8-0.39-0.56
CBR3-0.39-0.55

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG FOCAL ADHESION 201138All SZGR 2.0 genes in this pathway
KEGG NEUROTROPHIN SIGNALING PATHWAY 126103All SZGR 2.0 genes in this pathway
KEGG INSULIN SIGNALING PATHWAY 137103All SZGR 2.0 genes in this pathway
KEGG RENAL CELL CARCINOMA 7060All SZGR 2.0 genes in this pathway
BIOCARTA INTEGRIN PATHWAY 3829All SZGR 2.0 genes in this pathway
BIOCARTA MET PATHWAY 3730All SZGR 2.0 genes in this pathway
PID INSULIN PATHWAY 4532All SZGR 2.0 genes in this pathway
PID MET PATHWAY 8060All SZGR 2.0 genes in this pathway
PID REELIN PATHWAY 2929All SZGR 2.0 genes in this pathway
PID NECTIN PATHWAY 3020All SZGR 2.0 genes in this pathway
PID ECADHERIN NASCENT AJ PATHWAY 3933All SZGR 2.0 genes in this pathway
PID IFNG PATHWAY 4034All SZGR 2.0 genes in this pathway
PID PDGFRB PATHWAY 129103All SZGR 2.0 genes in this pathway
PID TRKR PATHWAY 6248All SZGR 2.0 genes in this pathway
PID PDGFRA PATHWAY 2218All SZGR 2.0 genes in this pathway
PID EPO PATHWAY 3429All SZGR 2.0 genes in this pathway
PID FAK PATHWAY 5945All SZGR 2.0 genes in this pathway
REACTOME SIGNALLING BY NGF 217167All SZGR 2.0 genes in this pathway
REACTOME ARMS MEDIATED ACTIVATION 1717All SZGR 2.0 genes in this pathway
REACTOME PROLONGED ERK ACTIVATION EVENTS 1918All SZGR 2.0 genes in this pathway
REACTOME NGF SIGNALLING VIA TRKA FROM THE PLASMA MEMBRANE 137105All SZGR 2.0 genes in this pathway
REACTOME SIGNALLING TO ERKS 3630All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY PDGF 12293All SZGR 2.0 genes in this pathway
REACTOME DOWNSTREAM SIGNAL TRANSDUCTION 9576All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY ILS 10786All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF SIGNALING BY CBL 1816All SZGR 2.0 genes in this pathway
REACTOME IL 3 5 AND GM CSF SIGNALING 4334All SZGR 2.0 genes in this pathway
REACTOME IMMUNE SYSTEM 933616All SZGR 2.0 genes in this pathway
REACTOME CYTOKINE SIGNALING IN IMMUNE SYSTEM 270204All SZGR 2.0 genes in this pathway
HUTTMANN B CLL POOR SURVIVAL UP 276187All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER 20Q13 AMPLIFICATION DN 180101All SZGR 2.0 genes in this pathway
PAPASPYRIDONOS UNSTABLE ATEROSCLEROTIC PLAQUE UP 5236All SZGR 2.0 genes in this pathway
ODONNELL METASTASIS UP 8258All SZGR 2.0 genes in this pathway
LIAO METASTASIS 539324All SZGR 2.0 genes in this pathway
ABE VEGFA TARGETS 2HR 3421All SZGR 2.0 genes in this pathway
MONNIER POSTRADIATION TUMOR ESCAPE UP 393244All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING 510309All SZGR 2.0 genes in this pathway
SENGUPTA EBNA1 ANTICORRELATED 17385All SZGR 2.0 genes in this pathway
MARTENS BOUND BY PML RARA FUSION 456287All SZGR 2.0 genes in this pathway
FIGUEROA AML METHYLATION CLUSTER 5 DN 5031All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP 430288All SZGR 2.0 genes in this pathway
KOINUMA TARGETS OF SMAD2 OR SMAD3 824528All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN 1080713All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A 770480All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP 489314All SZGR 2.0 genes in this pathway