Gene Page:RAPGEF1

Summary?
GeneID 2889
Symbol RAPGEF1
Synonyms C3G|GRF2
Description Rap guanine nucleotide exchange factor 1
Reference MIM:600303|HGNC:HGNC:4568|Ensembl:ENSG00000107263|HPRD:02627|Vega:OTTHUMG00000020829
Gene type protein-coding
Map location 9q34.3
Pascal p-value 0.57
Sherlock p-value 0.45
Fetal beta 1.056
DMG 2 (# studies)
eGene Cerebellar Hemisphere
Myers' cis & trans
Support CompositeSet
Darnell FMRP targets

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:GWASdb Genome-wide Association Studies GWASdb records for schizophrenia
CV:PGCnp Genome-wide Association Study GWAS
DMG:vanEijk_2014 Genome-wide DNA methylation analysis This 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_2014 Genome-wide DNA methylation analysis This 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

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg13655250 9 134544528 RAPGEF1 3.093E-4 0.615 0.04 DMG:Wockner_2014
cg27024922 9 134378058 RAPGEF1 9.58E-6 5.148 DMG:vanEijk_2014
cg25954354 9 133971548 RAPGEF1 9.282E-4 4.479 DMG:vanEijk_2014

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs12353112 chr9 133765871 RAPGEF1 2889 0.17 cis
rs1420486 chr8 132660693 RAPGEF1 2889 0.19 trans

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
死神:胎儿(13 - 26 postconception周),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
Gene Pearson's Correlation Spearman's Correlation
PITPNM1 0.82 0.81
CHRNA4 0.80 0.79
DNER 0.80 0.84
PLA2G15 0.79 0.80
SYT3 0.78 0.84
WNT4 0.77 0.70
PIP5KL1 0.76 0.78
RGS19 0.76 0.77
KCND2 0.76 0.76
WNT3 0.75 0.77
Top 10 negatively co-expressed genes
Gene Pearson'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 name Pathway size # SZGR 2.0 genes in pathway Info
KEGG FOCAL ADHESION 201 138 All SZGR 2.0 genes in this pathway
KEGG NEUROTROPHIN SIGNALING PATHWAY 126 103 All SZGR 2.0 genes in this pathway
KEGG INSULIN SIGNALING PATHWAY 137 103 All SZGR 2.0 genes in this pathway
KEGG RENAL CELL CARCINOMA 70 60 All SZGR 2.0 genes in this pathway
BIOCARTA INTEGRIN PATHWAY 38 29 All SZGR 2.0 genes in this pathway
BIOCARTA MET PATHWAY 37 30 All SZGR 2.0 genes in this pathway
PID INSULIN PATHWAY 45 32 All SZGR 2.0 genes in this pathway
PID MET PATHWAY 80 60 All SZGR 2.0 genes in this pathway
PID REELIN PATHWAY 29 29 All SZGR 2.0 genes in this pathway
PID NECTIN PATHWAY 30 20 All SZGR 2.0 genes in this pathway
PID ECADHERIN NASCENT AJ PATHWAY 39 33 All SZGR 2.0 genes in this pathway
PID IFNG PATHWAY 40 34 All SZGR 2.0 genes in this pathway
PID PDGFRB PATHWAY 129 103 All SZGR 2.0 genes in this pathway
PID TRKR PATHWAY 62 48 All SZGR 2.0 genes in this pathway
PID PDGFRA PATHWAY 22 18 All SZGR 2.0 genes in this pathway
PID EPO PATHWAY 34 29 All SZGR 2.0 genes in this pathway
PID FAK PATHWAY 59 45 All SZGR 2.0 genes in this pathway
REACTOME SIGNALLING BY NGF 217 167 All SZGR 2.0 genes in this pathway
REACTOME ARMS MEDIATED ACTIVATION 17 17 All SZGR 2.0 genes in this pathway
REACTOME PROLONGED ERK ACTIVATION EVENTS 19 18 All SZGR 2.0 genes in this pathway
REACTOME NGF SIGNALLING VIA TRKA FROM THE PLASMA MEMBRANE 137 105 All SZGR 2.0 genes in this pathway
REACTOME SIGNALLING TO ERKS 36 30 All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY PDGF 122 93 All SZGR 2.0 genes in this pathway
REACTOME DOWNSTREAM SIGNAL TRANSDUCTION 95 76 All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY ILS 107 86 All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF SIGNALING BY CBL 18 16 All SZGR 2.0 genes in this pathway
REACTOME IL 3 5 AND GM CSF SIGNALING 43 34 All SZGR 2.0 genes in this pathway
REACTOME IMMUNE SYSTEM 933 616 All SZGR 2.0 genes in this pathway
REACTOME CYTOKINE SIGNALING IN IMMUNE SYSTEM 270 204 All SZGR 2.0 genes in this pathway
HUTTMANN B CLL POOR SURVIVAL UP 276 187 All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER 20Q13 AMPLIFICATION DN 180 101 All SZGR 2.0 genes in this pathway
PAPASPYRIDONOS UNSTABLE ATEROSCLEROTIC PLAQUE UP 52 36 All SZGR 2.0 genes in this pathway
ODONNELL METASTASIS UP 82 58 All SZGR 2.0 genes in this pathway
LIAO METASTASIS 539 324 All SZGR 2.0 genes in this pathway
ABE VEGFA TARGETS 2HR 34 21 All SZGR 2.0 genes in this pathway
MONNIER POSTRADIATION TUMOR ESCAPE UP 393 244 All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING 510 309 All SZGR 2.0 genes in this pathway
SENGUPTA EBNA1 ANTICORRELATED 173 85 All SZGR 2.0 genes in this pathway
MARTENS BOUND BY PML RARA FUSION 456 287 All SZGR 2.0 genes in this pathway
FIGUEROA AML METHYLATION CLUSTER 5 DN 50 31 All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP 430 288 All SZGR 2.0 genes in this pathway
KOINUMA TARGETS OF SMAD2 OR SMAD3 824 528 All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN 1080 713 All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A 770 480 All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP 489 314 All SZGR 2.0 genes in this pathway