Gene Page: RARG

Summary ?
GeneID5916
SymbolRARG
SynonymsNR1B3|RARC
Descriptionretinoic acid receptor gamma
ReferenceMIM:180190|HGNC:HGNC:9866|Ensembl:ENSG00000172819|HPRD:01573|Vega:OTTHUMG00000048077
Gene typeprotein-coding
Map location12q13
Pascal p-value0.013
TADA p-value0.001
Fetal beta-1.111
DMG1 (# studies)
eGeneMyers' cis & trans
Meta
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). 1
DNM:Xu_2012Whole Exome Sequencing analysisDe novo mutations of 4 genes were identified by exome sequencing of 795 samples in this study

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
RARGchr1253608241TANM_000966
NM_001042728
NM_001243730
NM_001243731
NM_001243732		p.209K>*
p.198K>*
p.137K>*
p.88K>*
p.187K>*		nonsense
nonsense
nonsense
nonsense
nonsense		SchizophreniaDNM:Xu_2012

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg273643191253626837RARG9.92E-5-0.3780.028DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs16955618chr1529937543RARG59160.14trans

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
PDE6C0.500.29
TAS2R40.500.41
CILP0.500.44
TAS2R480.500.43
NAT80.490.39
TGM10.480.41
PLA2G4B0.480.39
MST1R0.480.42
AC034236.30.470.36
SLC4A50.470.45
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
IFI27-0.28-0.37
RRAS-0.28-0.37
ITM2A-0.28-0.35
GNG11-0.27-0.38
ABCG2-0.27-0.36
RP11-884K10.1-0.27-0.36
TM4SF18-0.27-0.33
MT-CO2-0.26-0.34
C1orf64-0.26-0.28
S100A4-0.26-0.35

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003700transcription factor activityIEA-
GO:0003707steroid hormone receptor activityIEA-
GO:0003708retinoic acid receptor activityTAS2157970 
GO:0005515protein bindingIPI10428834 
GO:0008270zinc ion bindingIEA-
GO:0046872metal ion bindingIEA-
GO:0046965retinoid X receptor bindingISS-
GO:0043565sequence-specific DNA bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0000122negative regulation of transcription from RNA polymerase II promoterISS-
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0006350transcriptionIEA-
GO:0008285negative regulation of cell proliferationISS-
GO:0008361regulation of cell sizeTAS18438858 
GO:0048048embryonic eye morphogenesisIEA-
GO:0007275multicellular organismal developmentTAS2157970 
GO:0043065positive regulation of apoptosisIEA-
GO:0048384retinoic acid receptor signaling pathwayIDA17943189 
GO:0032526response to retinoic acidIDA17943189 
GO:0035116embryonic hindlimb morphogenesisISS-
GO:0045944positive regulation of transcription from RNA polymerase II promoterIEA-
GO:0060070Wnt receptor signaling pathway through beta-cateninTAS18484682 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIEA-
GO:0005667transcription factor complexIEA-
GO:0016021integral to membraneNAS17943189 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PID RXR VDR PATHWAY 2624All SZGR 2.0 genes in this pathway
PID RETINOIC ACID PATHWAY 3023All SZGR 2.0 genes in this pathway
REACTOME GENERIC TRANSCRIPTION PATHWAY 352181All SZGR 2.0 genes in this pathway
REACTOME NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY 4936All SZGR 2.0 genes in this pathway
THUM SYSTOLIC HEART FAILURE UP 423283All SZGR 2.0 genes in this pathway
WANG BARRETTS ESOPHAGUS AND ESOPHAGUS CANCER DN 3722All SZGR 2.0 genes in this pathway
ZIRN TRETINOIN RESPONSE UP 2113All SZGR 2.0 genes in this pathway
AMUNDSON GENOTOXIC SIGNATURE 10568All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 2 DN 5142All SZGR 2.0 genes in this pathway
KIM MYCN AMPLIFICATION TARGETS UP 9264All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM1 229137All SZGR 2.0 genes in this pathway
SHIN B CELL LYMPHOMA CLUSTER 7 2722All SZGR 2.0 genes in this pathway
HOFMANN CELL LYMPHOMA DN 3929All SZGR 2.0 genes in this pathway
MURAKAMI UV RESPONSE 6HR DN 2113All SZGR 2.0 genes in this pathway
SARTIPY BLUNTED BY INSULIN RESISTANCE DN 1814All SZGR 2.0 genes in this pathway
MURAKAMI UV RESPONSE 24HR 2013All SZGR 2.0 genes in this pathway
MARTINEZ RB1 TARGETS UP 673430All SZGR 2.0 genes in this pathway
MARTINEZ TP53 TARGETS DN 593372All SZGR 2.0 genes in this pathway
MARTINEZ RB1 AND TP53 TARGETS DN 591366All SZGR 2.0 genes in this pathway
MCCABE BOUND BY HOXC6 469239All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING 510309All SZGR 2.0 genes in this pathway
MATTHEWS SKIN CARCINOGENESIS VIA JUN 1710All SZGR 2.0 genes in this pathway
PARK TRETINOIN RESPONSE AND PML RARA FUSION 3021All SZGR 2.0 genes in this pathway
AGUIRRE PANCREATIC CANCER COPY NUMBER DN 238145All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP 395249All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS DN 442275All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3 UNMETHYLATED 536296All SZGR 2.0 genes in this pathway
YAMASHITA LIVER CANCER STEM CELL UP 4738All SZGR 2.0 genes in this pathway
YAMASHITA LIVER CANCER STEM CELL DN 7651All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS VIA AKT1 DN 8251All SZGR 2.0 genes in this pathway
WANG NFKB TARGETS 2515All SZGR 2.0 genes in this pathway
DELACROIX RARG BOUND MEF 367231All SZGR 2.0 genes in this pathway
FOSTER KDM1A TARGETS DN 211119All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY 1839928All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-124/506657663m8hsa-miR-506UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brainUAAGGCACGCGGUGAAUGCC
hsa-miR-506UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brainUAAGGCACGCGGUGAAUGCC
miR-142-3p7117181A,m8hsa-miR-142-3pUGUAGUGUUUCCUACUUUAUGGA
miR-1821321391A,m8hsa-miR-182UUUGGCAAUGGUAGAACUCACA
hsa-miR-182UUUGGCAAUGGUAGAACUCACA
miR-24410416m8hsa-miR-24SZUGGCUCAGUUCAGCAGGAACAG
miR-30-5p102810351A,m8hsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA
hsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA
miR-326822828m8hsa-miR-326CCUCUGGGCCCUUCCUCCAG
miR-331884890m8hsa-miR-331brainGCCCCUGGGCCUAUCCUAGAA
miR-34/449273279m8hsa-miR-34abrainUGGCAGUGUCUUAGCUGGUUGUU
hsa-miR-34cAGGCAGUGUAGUUAGCUGAUUGC
hsa-miR-449UGGCAGUGUAUUGUUAGCUGGU
hsa-miR-449bAGGCAGUGUAUUGUUAGCUGGC
miR-961331391Ahsa-miR-96brainUUUGGCACUAGCACAUUUUUGC
hsa-miR-96brainUUUGGCACUAGCACAUUUUUGC