SZGR2

Summary ?

GeneID	2914
Symbol	GRM4
Synonyms	GPRC1D\|MGLUR4\|mGlu4
Description	glutamate receptor, metabotropic 4
Reference	MIM:604100\|HGNC:HGNC:4596\|Ensembl:ENSG00000124493\|HPRD:04978\|
Gene type	protein-coding
Map location	6p21.3
Pascal p-value	0.119
Sherlock p-value	0.722
Fetal beta	-0.155
eGene	Cerebellar Hemisphere Myers' cis & trans
Support	GPCR SIGNALLING CompositeSet Darnell FMRP targets Potential synaptic genes

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
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Association	A combined odds ratio method (Sun et al. 2008), association studies	1	Link to SZGene
GSMA_I	Genome scan meta-analysis	Psr: 0.033
GSMA_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.04433
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 5
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0018

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs17392743	chr1	54764240	GRM4	2914	0.01	trans
rs6687849	chr1	175904808	GRM4	2914	0	trans
rs2481653	chr1	176044120	GRM4	2914	0.05	trans
rs2502827	chr1	176044216	GRM4	2914	1.129E-5	trans
rs12405921	chr1	206695730	GRM4	2914	0.03	trans
rs17572651	chr1	218943612	GRM4	2914	1.145E-4	trans
snp_a-1919794		0	GRM4	2914	0.19	trans
rs882011	chr2	22711668	GRM4	2914	0.06	trans
rs16829545	chr2	151977407	GRM4	2914	1.247E-5	trans
rs3845734	chr2	171125572	GRM4	2914	2.083E-4	trans
rs7584986	chr2	184111432	GRM4	2914	2.423E-9	trans
rs6807632	chr3	111395567	GRM4	2914	0	trans
rs7635430	chr3	180152035	GRM4	2914	0.02	trans
rs6828371	chr4	15757600	GRM4	2914	0.12	trans
rs6826731	chr4	72130691	GRM4	2914	0.06	trans
rs2115110	chr5	38193428	GRM4	2914	0.12	trans
rs17762315	chr5	76807576	GRM4	2914	0	trans
rs7729096	chr5	76835927	GRM4	2914	0	trans
rs10063752	chr5	109259572	GRM4	2914	0.08	trans
rs1368303	chr5	147672388	GRM4	2914	1.145E-7	trans
rs1929769	chr6	40765977	GRM4	2914	0.13	trans
rs2530313	chr7	148112233	GRM4	2914	0.17	trans
rs17079498	chr8	3018343	GRM4	2914	0.02	trans
rs4872540	chr8	22598980	GRM4	2914	0.05	trans
rs6989594	chr8	126303866	GRM4	2914	0.02	trans
rs7021724	chr9	2527899	GRM4	2914	0.13	trans
rs2766987	chr9	113667956	GRM4	2914	0.12	trans
rs17263352	chr9	124811572	GRM4	2914	0.02	trans
rs12716680	chr13	42196469	GRM4	2914	0.12	trans
rs7996604	chr13	42224412	GRM4	2914	0.07	trans
snp_a-1880548		0	GRM4	2914	0.08	trans
rs1629937	chr14	77059671	GRM4	2914	0	trans
rs17104720	chr14	77127308	GRM4	2914	2.101E-6	trans
rs17104722	chr14	77138109	GRM4	2914	0.07	trans
rs17104782	chr14	77156735	GRM4	2914	0.07	trans
rs6574467	chr14	79179744	GRM4	2914	0.01	trans
rs10146003	chr14	79191170	GRM4	2914	0.01	trans
rs16955618	chr15	29937543	GRM4	2914	2.74E-23	trans
snp_a-1830894		0	GRM4	2914	6.868E-4	trans
rs16968252	chr17	31692447	GRM4	2914	0.08	trans
rs17823633	chr17	68851458	GRM4	2914	0.15	trans
rs17085767	chr18	69839397	GRM4	2914	0.1	trans
rs749043	chr20	46995700	GRM4	2914	0.2	trans
rs1041786	chr21	22617710	GRM4	2914	0.19	trans

Section II. Transcriptome annotation

General gene expression (GTEx)

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
Gene	Pearson's Correlation	Spearman's Correlation
TBC1D25	0.92	0.91
APBB1	0.91	0.90
AGAP3	0.91	0.89
AP2A2	0.91	0.91
EPN1	0.90	0.89
RTN1	0.90	0.88
CACNB3	0.89	0.89
SNAP47	0.89	0.84
MCOLN1	0.89	0.88
ASB6	0.89	0.89

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.21	-0.78	-0.71
MT-CO2	-0.77	-0.66
AF347015.31	-0.77	-0.66
AF347015.8	-0.77	-0.67
MT-CYB	-0.75	-0.65
AF347015.2	-0.74	-0.61
AF347015.26	-0.74	-0.63
AF347015.33	-0.74	-0.62
AF347015.27	-0.73	-0.66
AL139819.3	-0.72	-0.69

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004872	receptor activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007269	neurotransmitter secretion	TAS	neuron, axon, Synap, serotonin, Neurotransmitter, dopamine (GO term level: 8)	15102938
GO:0007268	synaptic transmission	IEA	neuron, Synap, Neurotransmitter (GO term level: 6)	-
GO:0007268	synaptic transmission	TAS	neuron, Synap, Neurotransmitter (GO term level: 6)	8738157
GO:0007196	metabotropic glutamate receptor, adenylate cyclase inhibiting pathway	IMP	glutamate (GO term level: 12)	15102938
GO:0043526	neuroprotection	TAS	neuron (GO term level: 9)	15102938
GO:0000187	activation of MAPK activity	IDA		15102938
GO:0007186	G-protein coupled receptor protein signaling pathway	IEA		-
GO:0007194	negative regulation of adenylate cyclase activity	IEP		15102938
GO:0007165	signal transduction	IEA		-
GO:0007612	learning	IEA		-
GO:0043410	positive regulation of MAPKKK cascade	IEP		15102938
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005622	intracellular	IDA		15102938
GO:0016021	integral to membrane	IEA		-
GO:0005886	plasma membrane	IEA		-
GO:0005887	integral to plasma membrane	IDA		15102938
GO:0031410	cytoplasmic vesicle	IDA		15102938

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION	272	195	All SZGR 2.0 genes in this pathway
KEGG TASTE TRANSDUCTION	52	28	All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY GPCR	920	449	All SZGR 2.0 genes in this pathway
REACTOME CLASS C 3 METABOTROPIC GLUTAMATE PHEROMONE RECEPTORS	15	11	All SZGR 2.0 genes in this pathway
REACTOME GPCR LIGAND BINDING	408	246	All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING	510	309	All SZGR 2.0 genes in this pathway
ZWANG CLASS 1 TRANSIENTLY INDUCED BY EGF	516	308	All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family	Target position			miRNA ID	miRNA seq
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-129-5p	668	674	1A	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
miR-129-5p	668	674	1A	hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-203.1	937	943	m8	hsa-miR-203	UGAAAUGUUUAGGACCACUAG
miR-29	122	128	m8	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU

SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.

Gene Page: GRM4