SZGR2

Summary ?

GeneID	2903
Symbol	GRIN2A
Synonyms	EPND\|FESD\|GluN2A\|LKS\|NMDAR2A\|NR2A
Description	glutamate ionotropic receptor NMDA type subunit 2A
Reference	MIM:138253\|HGNC:HGNC:4585\|Ensembl:ENSG00000183454\|HPRD:00698\|Vega:OTTHUMG00000129721
Gene type	protein-coding
Map location	16p13.2
Pascal p-value	2.298E-5
TADA p-value	0.024
DMG	2 (# studies)
Support	LIGAND GATED ION SIGNALING G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS G2Cdb.human_mGluR5 G2Cdb.human_TAP-PSD-95-CORE G2Cdb.humanNRC G2Cdb.humanPSD G2Cdb.humanPSP CompositeSet Darnell FMRP targets Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWAScat	Genome-wide Association Studies	This data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGC128	Genome-wide Association Study	A multi-stage schizophrenia GWAS of up to 36,989 cases and 113,075 controls. Reported by the Schizophrenia Working Group of PGC. 128 independent associations spanning 108 loci
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Jaffe_2016	Genome-wide DNA methylation analysis	This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05.	2
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).	2
DNM:Fromer_2014	Whole Exome Sequencing analysis	This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
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
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenics,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 15

Section I. Genetics and epigenetics annotation

CV:PGC128

SNP ID	Chromosome	Position	Allele	P	Function	Gene	Up/Down Distance
rs9922678	chr16	9946319	AG	6.721E-9	intronic	GRIN2A

DNM table

Gene	Chromosome	Position	Ref	Alt	Transcript	AA change	Mutation type	Sift	CG46	Trait	Study
GRIN2A	chr16	9857517	A	G	NM_000833 NM_001134407 NM_001134408	p.1295I>T p.1295I>T .	missense missense intronic			Schizophrenia	DNM:Fromer_2014

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg15134033	16	10274415	GRIN2A	1.887E-4	0.24	0.034	DMG:Wockner_2014
cg03764381	16	10275410	GRIN2A	1.61E-8	-0.009	5.96E-6	DMG:Jaffe_2016

Section II. Transcriptome annotation

General gene expression (GTEx)

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
ZFP36	0.64	0.67
MT2A	0.62	0.61
CXCL1	0.61	0.53
SAT1	0.61	0.58
GADD45B	0.59	0.60
FOSL1	0.59	0.52
MT1F	0.59	0.50
TLCD1	0.59	0.59
MT1G	0.59	0.57
FXYD1	0.58	0.60

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
CSRP2BP	-0.54	-0.55
PPP2R2D	-0.53	-0.57
ARFGAP2	-0.53	-0.53
PNMA1	-0.53	-0.56
WRNIP1	-0.52	-0.54
RAB1A	-0.52	-0.57
PSMD1	-0.52	-0.50
AC119673.2	-0.52	-0.51
FAM50B	-0.52	-0.54
BCL2L1	-0.52	-0.56

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004972	N-methyl-D-aspartate selective glutamate receptor activity	TAS	glutamate (GO term level: 8)	8768735
GO:0004970	ionotropic glutamate receptor activity	IEA	glutamate (GO term level: 7)	-
GO:0005234	extracellular-glutamate-gated ion channel activity	IEA	glutamate (GO term level: 11)	-
GO:0035254	glutamate receptor binding	IEA	glutamate (GO term level: 5)	-
GO:0000287	magnesium ion binding	IEA		-
GO:0004872	receptor activity	IEA		-
GO:0005509	calcium ion binding	IEA		-
GO:0005515	protein binding	IPI		17997397
GO:0005262	calcium channel activity	IEA		-
GO:0005216	ion channel activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0022008	neurogenesis	IEA	neurogenesis (GO term level: 6)	-
GO:0060079	regulation of excitatory postsynaptic membrane potential	IEA	neuron, Synap (GO term level: 10)	-
GO:0048167	regulation of synaptic plasticity	IEA	Synap (GO term level: 8)	-
GO:0007215	glutamate signaling pathway	TAS	glutamate (GO term level: 7)	8768735
GO:0030431	sleep	IEA	Brain (GO term level: 3)	-
GO:0042428	serotonin metabolic process	IEA	serotonin, Neurotransmitter (GO term level: 8)	-
GO:0042417	dopamine metabolic process	IEA	Neurotransmitter, dopamine (GO term level: 8)	-
GO:0001964	startle response	IEA		-
GO:0001975	response to amphetamine	IEA		-
GO:0008542	visual learning	IEA		-
GO:0009611	response to wounding	IEA		-
GO:0007613	memory	IEA		-
GO:0008104	protein localization	IEA		-
GO:0006816	calcium ion transport	IEA		-
GO:0006811	ion transport	IEA		-
GO:0042177	negative regulation of protein catabolic process	IEA		-
GO:0033058	directional locomotion	IEA		-
GO:0042493	response to drug	IEA		-
GO:0045471	response to ethanol	IDA		18445116
GO:0051930	regulation of sensory perception of pain	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0042734	presynaptic membrane	IEA	neuron, axon, Synap (GO term level: 5)	-
GO:0014069	postsynaptic density	IEA	Synap (GO term level: 10)	-
GO:0019717	synaptosome	IEA	Synap, Brain (GO term level: 7)	-
GO:0017146	N-methyl-D-aspartate selective glutamate receptor complex	IDA	glutamate, Synap (GO term level: 10)	10480938
GO:0045211	postsynaptic membrane	IEA	Synap, Neurotransmitter (GO term level: 5)	-
GO:0045202	synapse	IEA	neuron, Synap, Neurotransmitter, Glial (GO term level: 2)	-
GO:0005737	cytoplasm	IDA		18029348
GO:0016021	integral to membrane	IEA		-
GO:0005886	plasma membrane	IEA		-
GO:0005887	integral to plasma membrane	TAS		8768735
GO:0030054	cell junction	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ACTN1	FLJ40884	actinin, alpha 1	-	HPRD	11854440
DLG1	DKFZp761P0818 \| DKFZp781B0426 \| DLGH1 \| SAP97 \| dJ1061C18.1.1 \| hdlg	discs, large homolog 1 (Drosophila)	-	HPRD,BioGRID	12933808
DLG2	DKFZp781D1854 \| DKFZp781E0954 \| FLJ37266 \| MGC131811 \| PSD-93	discs, large homolog 2, chapsyn-110 (Drosophila)	-	HPRD	10648730
DLG2	DKFZp781D1854 \| DKFZp781E0954 \| FLJ37266 \| MGC131811 \| PSD-93	discs, large homolog 2, chapsyn-110 (Drosophila)	Two-hybrid	BioGRID	9278515
DLG3	KIAA1232 \| MRX \| MRX90 \| NE-Dlg \| NEDLG \| SAP102	discs, large homolog 3 (neuroendocrine-dlg, Drosophila)	in vitro in vivo Two-hybrid	BioGRID	9278515 \|11937501
DLG3	KIAA1232 \| MRX \| MRX90 \| NE-Dlg \| NEDLG \| SAP102	discs, large homolog 3 (neuroendocrine-dlg, Drosophila)	-	HPRD	11937501 \|12070168
DLG4	FLJ97752 \| FLJ98574 \| PSD95 \| SAP90	discs, large homolog 4 (Drosophila)	-	HPRD	7569905 \|11937501 \|12419528
DLG4	FLJ97752 \| FLJ98574 \| PSD95 \| SAP90	discs, large homolog 4 (Drosophila)	Affinity Capture-Western in vitro in vivo Reconstituted Complex Two-hybrid	BioGRID	7569905 \|9278515 \|9286858 \|10648730 \|11937501 \|12419528
DLGAP1	DAP-1 \| DAP-1-ALPHA \| DAP-1-BETA \| GKAP \| MGC88156 \| SAPAP1 \| hGKAP	discs, large (Drosophila) homolog-associated protein 1	-	HPRD,BioGRID	9286858
FYN	MGC45350 \| SLK \| SYN	FYN oncogene related to SRC, FGR, YES	Affinity Capture-Western Reconstituted Complex	BioGRID	9892651 \|10458595 \|12419528 \|12932824
FYN	MGC45350 \| SLK \| SYN	FYN oncogene related to SRC, FGR, YES	-	HPRD	10458595 \|12932824
GRIN1	NMDA1 \| NMDAR1 \| NR1	glutamate receptor, ionotropic, N-methyl D-aspartate 1	NR1a interacts with NR2A.	BIND	11279200
GRIN1	NMDA1 \| NMDAR1 \| NR1	glutamate receptor, ionotropic, N-methyl D-aspartate 1	-	HPRD	8139656 \|10862698 \|11803122 \|12068077 \|12191494 \|12893641 \|14732708
GRIN1	NMDA1 \| NMDAR1 \| NR1	glutamate receptor, ionotropic, N-methyl D-aspartate 1	Affinity Capture-Western	BioGRID	12391275
GRIN3B	NR3B	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	Affinity Capture-Western	BioGRID	12008020
IL16	FLJ16806 \| FLJ42735 \| FLJ44234 \| HsT19289 \| IL-16 \| LCF \| prIL-16	interleukin 16 (lymphocyte chemoattractant factor)	npro-IL-16 interacts with NR2A.	BIND	12923170
IL16	FLJ16806 \| FLJ42735 \| FLJ44234 \| HsT19289 \| IL-16 \| LCF \| prIL-16	interleukin 16 (lymphocyte chemoattractant factor)	-	HPRD,BioGRID	10479680
INADL	Cipp \| FLJ26982 \| InaD-like \| PATJ	InaD-like (Drosophila)	-	HPRD	9647694
PTK2B	CADTK \| CAKB \| FADK2 \| FAK2 \| FRNK \| PKB \| PTK \| PYK2 \| RAFTK	PTK2B protein tyrosine kinase 2 beta	-	HPRD,BioGRID	11478920
PTPN4	PTPMEG \| PTPMEG1	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	-	HPRD,BioGRID	10748123
RICS	GC-GAP \| GRIT \| KIAA0712 \| MGC1892 \| p200RhoGAP \| p250GAP	Rho GTPase-activating protein	-	HPRD	12531901
SRC	ASV \| SRC1 \| c-SRC \| p60-Src	v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian)	Affinity Capture-Western Reconstituted Complex	BioGRID	10458595 \|12932824
SRC	ASV \| SRC1 \| c-SRC \| p60-Src	v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian)	-	HPRD	10458595 \|10884433 \|12932824

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG CALCIUM SIGNALING PATHWAY	178	134	All SZGR 2.0 genes in this pathway
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION	272	195	All SZGR 2.0 genes in this pathway
KEGG LONG TERM POTENTIATION	70	57	All SZGR 2.0 genes in this pathway
KEGG ALZHEIMERS DISEASE	169	110	All SZGR 2.0 genes in this pathway
KEGG AMYOTROPHIC LATERAL SCLEROSIS ALS	53	43	All SZGR 2.0 genes in this pathway
KEGG SYSTEMIC LUPUS ERYTHEMATOSUS	140	100	All SZGR 2.0 genes in this pathway
BIOCARTA NOS1 PATHWAY	24	21	All SZGR 2.0 genes in this pathway
PID REELIN PATHWAY	29	29	All SZGR 2.0 genes in this pathway
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES	186	155	All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM	279	221	All SZGR 2.0 genes in this pathway
REACTOME NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL	137	110	All SZGR 2.0 genes in this pathway
REACTOME RAS ACTIVATION UOPN CA2 INFUX THROUGH NMDA RECEPTOR	17	15	All SZGR 2.0 genes in this pathway
REACTOME ACTIVATION OF NMDA RECEPTOR UPON GLUTAMATE BINDING AND POSTSYNAPTIC EVENTS	37	32	All SZGR 2.0 genes in this pathway
REACTOME CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF RAS	27	23	All SZGR 2.0 genes in this pathway
REACTOME POST NMDA RECEPTOR ACTIVATION EVENTS	33	28	All SZGR 2.0 genes in this pathway
REACTOME UNBLOCKING OF NMDA RECEPTOR GLUTAMATE BINDING AND ACTIVATION	15	14	All SZGR 2.0 genes in this pathway
REACTOME CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF CAMKII	15	14	All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA WITH LMP1 DN	175	82	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP	485	293	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
AMUNDSON GENOTOXIC SIGNATURE	105	68	All SZGR 2.0 genes in this pathway
HATADA METHYLATED IN LUNG CANCER UP	390	236	All SZGR 2.0 genes in this pathway
WONG IFNA2 RESISTANCE DN	34	20	All SZGR 2.0 genes in this pathway
PENG GLUTAMINE DEPRIVATION DN	337	230	All SZGR 2.0 genes in this pathway
LU AGING BRAIN DN	153	120	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
LABBE WNT3A TARGETS DN	97	53	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3 UNMETHYLATED	536	296	All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3	590	403	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP	548	370	All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY	1839	928	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-125/351	904	910	m8	hsa-miR-125b^brain	UCCCUGAGACCCUAACUUGUGA
miR-125/351	904	910	m8	hsa-miR-125a^brain	UCCCUGAGACCCUUUAACCUGUG
miR-137	416	423	1A,m8	hsa-miR-137	UAUUGCUUAAGAAUACGCGUAG
miR-19	142	149	1A,m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	142	149	1A,m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-381	911	917	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-431	656	662	1A	hsa-miR-431	UGUCUUGCAGGCCGUCAUGCA
miR-7	166	172	1A	hsa-miR-7^SZ	UGGAAGACUAGUGAUUUUGUUG

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: GRIN2A