Gene Page: ARHGEF11

Summary ?
GeneID9826
SymbolARHGEF11
SynonymsGTRAP48|PDZ-RHOGEF
DescriptionRho guanine nucleotide exchange factor 11
ReferenceMIM:605708|HGNC:HGNC:14580|Ensembl:ENSG00000132694|HPRD:09302|Vega:OTTHUMG00000041292
Gene typeprotein-coding
Map location1q21
Sherlock p-value0.519
Fetal beta-0.636
eGeneMyers' cis & trans
SupportCompositeSet
Darnell FMRP targets
Ascano FMRP targets
Potential synaptic genes

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DNM:Fromer_2014Whole Exome Sequencing analysisThis study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
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: 0.0235 
GSMA_IIAGenome scan meta-analysis (All samples)Psr: 0.00814 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
ARHGEF11chr1156911204GANM_014784
NM_198236		.
.		silent
silent		SchizophreniaDNM:Fromer_2014
ARHGEF11chr1156918274GANM_014784
NM_198236		p.608R>C
p.648R>C		missense
missense		SchizophreniaDNM:Fromer_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs6128541chr2057917688ARHGEF1198260.07trans

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
SNAP470.860.81
TMEM55B0.850.80
TOMM40L0.840.79
ATG4B0.840.80
ARFIP20.840.74
UBL4A0.830.78
ST3GAL30.830.81
C7orf200.820.78
TBRG40.820.76
GSK3A0.820.77
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.21-0.71-0.64
AF347015.8-0.70-0.60
MT-CO2-0.68-0.58
AF347015.18-0.67-0.63
AF347015.26-0.67-0.58
MT-CYB-0.67-0.59
AF347015.2-0.67-0.57
AF347015.31-0.67-0.58
MT-ATP8-0.66-0.64
AF347015.27-0.66-0.61

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005089Rho guanyl-nucleotide exchange factor activityIEA-
GO:0005089Rho guanyl-nucleotide exchange factor activityTAS10026210 
GO:0005085guanyl-nucleotide exchange factor activityIEA-
GO:0001664G-protein-coupled receptor bindingIDA15755723 
GO:0004871signal transducer activityIEA-
GO:0005096GTPase activator activityIEA-
GO:0005515protein bindingIEA-
GO:0005515protein bindingIPI10026210 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0001558regulation of cell growthNAS10026210 
GO:0000910cytokinesisNAS10026210 
GO:0007186G-protein coupled receptor protein signaling pathwayTAS10026210 
GO:0030010establishment of cell polarityNAS10026210 
GO:0006941striated muscle contractionNAS10026210 
GO:0006928cell motionNAS10026210 
GO:0030036actin cytoskeleton organizationNAS10026210 
GO:0035023regulation of Rho protein signal transductionIEA-
GO:0045893positive regulation of transcription, DNA-dependentIDA10026210 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005622intracellularIC10026210 
GO:0005622intracellularIEA-
GO:0005737cytoplasmIDA15755723 
GO:0016020membraneIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG VASCULAR SMOOTH MUSCLE CONTRACTION 11581All SZGR 2.0 genes in this pathway
BIOCARTA MYOSIN PATHWAY 3122All SZGR 2.0 genes in this pathway
BIOCARTA RHO PATHWAY 3223All SZGR 2.0 genes in this pathway
BIOCARTA PAR1 PATHWAY 3728All SZGR 2.0 genes in this pathway
SIG CHEMOTAXIS 4537All SZGR 2.0 genes in this pathway
ST GA13 PATHWAY 3732All SZGR 2.0 genes in this pathway
PID RHOA REG PATHWAY 4630All SZGR 2.0 genes in this pathway
PID FAK PATHWAY 5945All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY RHO GTPASES 11381All SZGR 2.0 genes in this pathway
REACTOME SIGNALLING BY NGF 217167All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY 396292All SZGR 2.0 genes in this pathway
REACTOME NRAGE SIGNALS DEATH THROUGH JNK 4333All SZGR 2.0 genes in this pathway
REACTOME CELL DEATH SIGNALLING VIA NRAGE NRIF AND NADE 6043All SZGR 2.0 genes in this pathway
REACTOME P75 NTR RECEPTOR MEDIATED SIGNALLING 8161All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY GPCR 920449All SZGR 2.0 genes in this pathway
REACTOME AXON GUIDANCE 251188All SZGR 2.0 genes in this pathway
REACTOME G ALPHA1213 SIGNALLING EVENTS 7456All SZGR 2.0 genes in this pathway
REACTOME GPCR DOWNSTREAM SIGNALING 805368All SZGR 2.0 genes in this pathway
REACTOME SEMA4D IN SEMAPHORIN SIGNALING 3222All SZGR 2.0 genes in this pathway
REACTOME SEMAPHORIN INTERACTIONS 6853All SZGR 2.0 genes in this pathway
REACTOME SEMA4D INDUCED CELL MIGRATION AND GROWTH CONE COLLAPSE 2721All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN 335193All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 SIGNATURE 3 UP 341197All SZGR 2.0 genes in this pathway
LOCKWOOD AMPLIFIED IN LUNG CANCER 214139All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR DN 504323All SZGR 2.0 genes in this pathway
MCCABE BOUND BY HOXC6 469239All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 LCP WITH H3K4ME3 16280All SZGR 2.0 genes in this pathway
MIKKELSEN MEF LCP WITH H3K4ME3 12868All SZGR 2.0 genes in this pathway
MIKKELSEN IPS LCP WITH H3K4ME3 174100All SZGR 2.0 genes in this pathway
MIKKELSEN ES LCP WITH H3K4ME3 14280All SZGR 2.0 genes in this pathway
MIKKELSEN NPC LCP WITH H3K4ME3 5834All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-1289951001m8hsa-miR-128aUCACAGUGAACCGGUCUCUUUU
hsa-miR-128bUCACAGUGAACCGGUCUCUUUC
miR-132/21210701076m8hsa-miR-212SZUAACAGUCUCCAGUCACGGCC
hsa-miR-132brainUAACAGUCUACAGCCAUGGUCG
miR-17-5p/20/93.mr/106/519.d374380m8hsa-miR-17-5pCAAAGUGCUUACAGUGCAGGUAGU
hsa-miR-20abrainUAAAGUGCUUAUAGUGCAGGUAG
hsa-miR-106aAAAAGUGCUUACAGUGCAGGUAGC
hsa-miR-106bSZUAAAGUGCUGACAGUGCAGAU
hsa-miR-20bSZCAAAGUGCUCAUAGUGCAGGUAG
hsa-miR-519dCAAAGUGCCUCCCUUUAGAGUGU