SZGR2

Summary ?

GeneID	2902
Symbol	GRIN1
Synonyms	GluN1\|MRD8\|NMD-R1\|NMDA1\|NMDAR1\|NR1
Description	glutamate ionotropic receptor NMDA type subunit 1
Reference	MIM:138249\|HGNC:HGNC:4584\|Ensembl:ENSG00000176884\|HPRD:15926\|Vega:OTTHUMG00000020976
Gene type	protein-coding
Map location	9q34.3
Pascal p-value	0.108
Sherlock p-value	0.397
Fetal beta	-1.27
eGene	Myers' cis & trans
Support	LIGAND GATED ION SIGNALING G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS G2Cdb.human_PocklingtonH1 G2Cdb.human_TAP-PSD-95-CORE G2Cdb.humanNRC CompositeSet Darnell FMRP targets Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
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	2	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
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 7.9864

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs3823720	chr7	42001170	GRIN1	2902		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
AC021914.1	0.74	0.28
CLEC2B	0.64	0.35
CXCL2	0.61	0.53
AL050337.1	0.57	0.18
AC137766.1	0.56	0.37
C1orf61	0.55	0.34
C17orf84	0.54	0.03
OASL	0.53	0.33
C1orf54	0.52	0.31
IFITM1	0.51	0.47

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
DNAJC7	-0.51	-0.38
CHMP4B	-0.50	-0.35
ARFGAP2	-0.50	-0.40
NUDC	-0.49	-0.40
NDUFS2	-0.48	-0.36
UBE2Q1	-0.48	-0.37
GRPEL1	-0.48	-0.40
C20orf43	-0.47	-0.36
SPG7	-0.47	-0.29
MRPS5	-0.47	-0.41

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004972	N-methyl-D-aspartate selective glutamate receptor activity	IDA	glutamate (GO term level: 8)	7679115 \|7685113
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:0016595	glutamate binding	IDA	glutamate (GO term level: 5)	7685113
GO:0035254	glutamate receptor binding	ISS	glutamate (GO term level: 5)	-
GO:0000287	magnesium ion binding	IEA		-
GO:0004872	receptor activity	IEA		-
GO:0005509	calcium ion binding	ISS		-
GO:0005516	calmodulin binding	ISS		-
GO:0005262	calcium channel activity	IDA		7685113
GO:0005216	ion channel activity	IEA		-
GO:0016594	glycine binding	IDA		7685113
GO:0016594	glycine binding	IMP		17047094
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0060079	regulation of excitatory postsynaptic membrane potential	ISS	neuron, Synap (GO term level: 10)	-
GO:0007268	synaptic transmission	ISS	neuron, Synap, Neurotransmitter (GO term level: 6)	-
GO:0035235	ionotropic glutamate receptor signaling pathway	ISS	glutamate (GO term level: 8)	-
GO:0008542	visual learning	ISS		-
GO:0006811	ion transport	IEA		-
GO:0006812	cation transport	IDA		7685113
GO:0042391	regulation of membrane potential	IDA		7679115 \|7685113 \|17047094
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	ISS		-
GO:0045471	response to ethanol	IDA		18445116
GO:0055074	calcium ion homeostasis	ISS		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0008021	synaptic vesicle	ISS	Synap, Neurotransmitter (GO term level: 12)	-
GO:0014069	postsynaptic density	ISS	Synap (GO term level: 10)	-
GO:0019717	synaptosome	ISS	Synap, Brain (GO term level: 7)	-
GO:0017146	N-methyl-D-aspartate selective glutamate receptor complex	IDA	glutamate, Synap (GO term level: 10)	7679115 \|10480938 \|17047094
GO:0030425	dendrite	IDA	neuron, axon, dendrite (GO term level: 6)	10749211
GO:0045211	postsynaptic membrane	IEA	Synap, Neurotransmitter (GO term level: 5)	-
GO:0045211	postsynaptic membrane	ISS	Synap, Neurotransmitter (GO term level: 5)	-
GO:0045202	synapse	IEA	neuron, Synap, Neurotransmitter, Glial (GO term level: 2)	-
GO:0045202	synapse	ISS	neuron, Synap, Neurotransmitter, Glial (GO term level: 2)	-
GO:0016021	integral to membrane	IEA		-
GO:0005886	plasma membrane	IEA		-
GO:0005887	integral to plasma membrane	IDA		7685113
GO:0030054	cell junction	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ACTN2	CMD1AA	actinin, alpha 2	-	HPRD	9009191 \|9728925 \|9952395
ACTN2	CMD1AA	actinin, alpha 2	alpha-actinin-2 interacts with NR1A. This interaction was modeled on a demonstrated interaction between human alpha-actinin-2 and NR1A from an unspecified species.	BIND	9009191
AKAP9	AKAP350 \| AKAP450 \| CG-NAP \| HYPERION \| KIAA0803 \| MU-RMS-40.16A \| PRKA9 \| YOTIAO	A kinase (PRKA) anchor protein (yotiao) 9	-	HPRD	9482789\|10862698
AKAP9	AKAP350 \| AKAP450 \| CG-NAP \| HYPERION \| KIAA0803 \| MU-RMS-40.16A \| PRKA9 \| YOTIAO	A kinase (PRKA) anchor protein (yotiao) 9	-	HPRD	10862698
CACNG2	MGC138502 \| MGC138504	calcium channel, voltage-dependent, gamma subunit 2	Co-fractionation	BioGRID	11140673
CAMK2A	CAMKA \| KIAA0968	calcium/calmodulin-dependent protein kinase II alpha	-	HPRD	10862698
CANX	CNX \| FLJ26570 \| IP90 \| P90	calnexin	-	HPRD	11506858 \|14732708
CDH2	CD325 \| CDHN \| CDw325 \| NCAD	cadherin 2, type 1, N-cadherin (neuronal)	-	HPRD	10862698
CIT	CRIK \| KIAA0949 \| STK21	citron (rho-interacting, serine/threonine kinase 21)	-	HPRD	10862698
CLTC	CHC \| CHC17 \| CLH-17 \| CLTCL2 \| Hc \| KIAA0034	clathrin, heavy chain (Hc)	-	HPRD	10862698
CTNNB1	CTNNB \| DKFZp686D02253 \| FLJ25606 \| FLJ37923	catenin (cadherin-associated protein), beta 1, 88kDa	-	HPRD	10862698
DLG2	DKFZp781D1854 \| DKFZp781E0954 \| FLJ37266 \| MGC131811 \| PSD-93	discs, large homolog 2, chapsyn-110 (Drosophila)	-	HPRD	10862698
DLG3	KIAA1232 \| MRX \| MRX90 \| NE-Dlg \| NEDLG \| SAP102	discs, large homolog 3 (neuroendocrine-dlg, Drosophila)	-	HPRD	10862698
DLG4	FLJ97752 \| FLJ98574 \| PSD95 \| SAP90	discs, large homolog 4 (Drosophila)	-	HPRD	9009191 \|9502803 \|11506858 \|12068077 \|14732708 \|15030493
DLGAP4	DAP4 \| KIAA0964 \| MGC131862 \| RP5-977B1.6 \| SAPAP4	discs, large (Drosophila) homolog-associated protein 4	-	HPRD	10862698
DNM1	DNM	dynamin 1	-	HPRD	10862698
DRD1	DADR \| DRD1A	dopamine receptor D1	-	HPRD	12408866
DUSP4	HVH2 \| MKP-2 \| MKP2 \| TYP	dual specificity phosphatase 4	-	HPRD	10862698
EPHB2	CAPB \| DRT \| EPHT3 \| ERK \| Hek5 \| MGC87492 \| PCBC \| Tyro5	EPH receptor B2	-	HPRD	11754835
EPHB4	HTK \| MYK1 \| TYRO11	EPH receptor B4	-	HPRD	11136979
FUS	CHOP \| FUS-CHOP \| FUS1 \| TLS \| TLS/CHOP \| hnRNP-P2	fusion (involved in t(12;16) in malignant liposarcoma)	-	HPRD	10862698
GRIN2A	NMDAR2A \| NR2A	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	NR1a interacts with NR2A.	BIND	11279200
GRIN2A	NMDAR2A \| NR2A	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	-	HPRD	8139656 \|10862698 \|11803122 \|12068077 \|12191494 \|12893641 \|14732708
GRIN2A	NMDAR2A \| NR2A	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	Affinity Capture-Western	BioGRID	12391275
GRIN2B	MGC142178 \| MGC142180 \| NMDAR2B \| NR2B \| hNR3	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	Affinity Capture-Western	BioGRID	12391275
GRIN2B	MGC142178 \| MGC142180 \| NMDAR2B \| NR2B \| hNR3	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	-	HPRD	8139656 \|12191494 \|15030493
GRIN2D	EB11 \| NMDAR2D	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	-	HPRD	12191494
GRIN3A	FLJ45414 \| NMDAR-L \| NR3A	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	Affinity Capture-Western	BioGRID	12391275
GRIN3A	FLJ45414 \| NMDAR-L \| NR3A	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	-	HPRD	9620802 \|11160393 \|11588171
GRIN3B	NR3B	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	Affinity Capture-Western	BioGRID	12008020
HNRNPU	HNRPU \| SAF-A \| U21.1	heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)	-	HPRD	10862698
HRAS	C-BAS/HAS \| C-H-RAS \| C-HA-RAS1 \| CTLO \| H-RASIDX \| HAMSV \| HRAS1 \| K-RAS \| N-RAS \| RASH1	v-Ha-ras Harvey rat sarcoma viral oncogene homolog	-	HPRD	10862698
HSPA1A	FLJ54303 \| FLJ54370 \| FLJ54392 \| FLJ54408 \| FLJ75127 \| HSP70-1 \| HSP70-1A \| HSP70I \| HSP72 \| HSPA1 \| HSPA1B	heat shock 70kDa protein 1A	-	HPRD	10862698
INA	FLJ18662 \| FLJ57501 \| MGC12702 \| NEF5 \| NF-66 \| TXBP-1	internexin neuronal intermediate filament protein, alpha	-	HPRD	10862698
KAT5	ESA1 \| HTATIP \| HTATIP1 \| PLIP \| TIP \| TIP60 \| cPLA2	K(lysine) acetyltransferase 5	-	HPRD	10862698
MAP2	DKFZp686I2148 \| MAP2A \| MAP2B \| MAP2C	microtubule-associated protein 2	-	HPRD	10862698
MAP2K2	FLJ26075 \| MAPKK2 \| MEK2 \| MKK2 \| PRKMK2	mitogen-activated protein kinase kinase 2	-	HPRD	10862698
MYH9	DFNA17 \| EPSTS \| FTNS \| MGC104539 \| MHA \| NMHC-II-A \| NMMHCA	myosin, heavy chain 9, non-muscle	-	HPRD	10862698
NANOS1	NOS1	nanos homolog 1 (Drosophila)	-	HPRD	10862698
ND2	MTND2	NADH dehydrogenase, subunit 2 (complex I)	Affinity Capture-Western	BioGRID	15069201
NEFL	CMT1F \| CMT2E \| FLJ53642 \| NF-L \| NF68 \| NFL	neurofilament, light polypeptide	-	HPRD	9425014
NF1	DKFZp686J1293 \| FLJ21220 \| NFNS \| VRNF \| WSS	neurofibromin 1	-	HPRD	10862698
PLAT	DKFZp686I03148 \| T-PA \| TPA	plasminogen activator, tissue	-	HPRD	15448144
PPP2R1A	MGC786 \| PR65A	protein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform	-	HPRD	10862698
PPP2R2A	B55-ALPHA \| B55A \| FLJ26613 \| MGC52248 \| PR52A \| PR55A	protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform	-	HPRD	10862698
PRKCB	MGC41878 \| PKC-beta \| PKCB \| PRKCB1 \| PRKCB2	protein kinase C, beta	-	HPRD	10862698
PRKCE	MGC125656 \| MGC125657 \| PKCE \| nPKC-epsilon	protein kinase C, epsilon	-	HPRD	10862698
PRKCG	MGC57564 \| PKC-gamma \| PKCC \| PKCG \| SCA14	protein kinase C, gamma	-	HPRD	10862698
RAP2A	K-REV \| KREV \| RAP2 \| RbBP-30	RAP2A, member of RAS oncogene family	-	HPRD	10862698
RPS6KA3	CLS \| HU-3 \| ISPK-1 \| MAPKAPK1B \| MRX19 \| RSK \| RSK2 \| S6K-alpha3 \| p90-RSK2 \| pp90RSK2	ribosomal protein S6 kinase, 90kDa, polypeptide 3	-	HPRD	10862698
SP1	-	Sp1 transcription factor	-	HPRD	14970236
SP3	DKFZp686O1631 \| SPR-2	Sp3 transcription factor	-	HPRD	14970236
SPTAN1	(ALPHA)II-SPECTRIN \| FLJ44613 \| NEAS	spectrin, alpha, non-erythrocytic 1 (alpha-fodrin)	-	HPRD	9670010 \|10862698
SYNGAP1	DKFZp761G1421 \| KIAA1938 \| RASA1 \| RASA5 \| SYNGAP	synaptic Ras GTPase activating protein 1 homolog (rat)	-	HPRD	10862698
TIAM1	FLJ36302	T-cell lymphoma invasion and metastasis 1	Tiam1 interacts with NMDA subunit NR1. This interaction was modelled on a demonstrated interaction between human Tiam1 and NR1 from an unspecified species.	BIND	15721239
TJP1	DKFZp686M05161 \| MGC133289 \| ZO-1	tight junction protein 1 (zona occludens 1)	-	HPRD	10862698
TRAF3	CAP-1 \| CD40bp \| CRAF1 \| LAP1	TNF receptor-associated factor 3	-	HPRD	10862698
TUBA4B	FLJ13940 \| TUBA4	tubulin, alpha 4b (pseudogene)	-	HPRD	10862698

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 HUNTINGTONS DISEASE	185	109	All SZGR 2.0 genes in this pathway
BIOCARTA EPONFKB PATHWAY	11	11	All SZGR 2.0 genes in this pathway
BIOCARTA NOS1 PATHWAY	24	21	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
HAMAI APOPTOSIS VIA TRAIL DN	186	107	All SZGR 2.0 genes in this pathway
EBAUER TARGETS OF PAX3 FOXO1 FUSION UP	207	128	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
CHIARETTI ACUTE LYMPHOBLASTIC LEUKEMIA ZAP70	67	33	All SZGR 2.0 genes in this pathway
MCCLUNG DELTA FOSB TARGETS 8WK	47	38	All SZGR 2.0 genes in this pathway
ULE SPLICING VIA NOVA2	43	38	All SZGR 2.0 genes in this pathway
LEE CALORIE RESTRICTION NEOCORTEX DN	88	58	All SZGR 2.0 genes in this pathway
MARIADASON RESPONSE TO BUTYRATE SULINDAC 6	52	32	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS PTEN UP	181	112	All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D UP	210	124	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K27ME3	341	243	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 1HR DN	222	147	All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP	857	456	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-15/16/195/424/497	58	64	m8	hsa-miR-15a^brain	UAGCAGCACAUAAUGGUUUGUG
				hsa-miR-16^brain	UAGCAGCACGUAAAUAUUGGCG
				hsa-miR-15b^brain	UAGCAGCACAUCAUGGUUUACA
				hsa-miR-195^SZ	UAGCAGCACAGAAAUAUUGGC
				hsa-miR-424	CAGCAGCAAUUCAUGUUUUGAA
				hsa-miR-497	CAGCAGCACACUGUGGUUUGU
miR-214	56	62	m8	hsa-miR-214^brain	ACAGCAGGCACAGACAGGCAG

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: GRIN1