SZGR2

Summary ?

GeneID	2898
Symbol	GRIK2
Synonyms	EAA4\|GLR6\|GLUK6\|GLUR6\|GluK2\|MRT6
Description	glutamate ionotropic receptor kainate type subunit 2
Reference	MIM:138244\|HGNC:HGNC:4580\|Ensembl:ENSG00000164418\|HPRD:00692\|Vega:OTTHUMG00000016328
Gene type	protein-coding
Map location	6q16.3
Pascal p-value	0.002
Fetal beta	1.717
Support	LIGAND GATED ION SIGNALING G2Cdb.human_PocklingtonH1 G2Cdb.human_TAP-PSD-95-CORE G2Cdb.humanNRC G2Cdb.humanPSD G2Cdb.humanPSP 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
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: 7
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 15.5

Section I. Genetics and epigenetics annotation

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
MTMR9	0.88	0.93
NRXN1	0.88	0.92
CPEB4	0.88	0.92
KIAA0317	0.88	0.93
INPP4A	0.88	0.92
GABRB3	0.87	0.92
ATRN	0.87	0.92
AVL9	0.87	0.92
GNAQ	0.87	0.91
ATP9A	0.87	0.92

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.31	-0.65	-0.74
FXYD1	-0.65	-0.71
MT-CO2	-0.64	-0.75
HIGD1B	-0.63	-0.74
AC021016.1	-0.63	-0.71
AF347015.33	-0.63	-0.69
COPZ2	-0.62	-0.67
AF347015.8	-0.62	-0.73
MT-CYB	-0.62	-0.70
AF347015.27	-0.62	-0.70

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005234	extracellular-glutamate-gated ion channel activity	IEA	glutamate (GO term level: 11)	-
GO:0015277	kainate selective glutamate receptor activity	IDA	glutamate (GO term level: 8)	15537878
GO:0004872	receptor activity	IEA		-
GO:0005216	ion channel activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0048172	regulation of short-term neuronal synaptic plasticity	IMP	neuron, Synap (GO term level: 10)	15537878
GO:0007215	glutamate signaling pathway	TAS	glutamate (GO term level: 7)	7536611
GO:0050806	positive regulation of synaptic transmission	IMP	neuron, Synap (GO term level: 9)	15537878
GO:0051402	neuron apoptosis	IDA	neuron, axon, dendrite (GO term level: 7)	15537878
GO:0006811	ion transport	IEA		-
GO:0031557	induction of programmed cell death in response to chemical stimulus	NAS		15537878
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0045211	postsynaptic membrane	IEA	Synap, Neurotransmitter (GO term level: 5)	-
GO:0045202	synapse	IEA	neuron, Synap, Neurotransmitter, Glial (GO term level: 2)	-
GO:0005886	plasma membrane	IEA		-
GO:0005887	integral to plasma membrane	TAS		7536611
GO:0030054	cell junction	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
CASK	CAGH39 \| CMG \| FLJ22219 \| FLJ31914 \| LIN2 \| MICPCH \| TNRC8	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	-	HPRD	12151522
CDH2	CD325 \| CDHN \| CDw325 \| NCAD	cadherin 2, type 1, N-cadherin (neuronal)	-	HPRD	12151522
CTNNB1	CTNNB \| DKFZp686D02253 \| FLJ25606 \| FLJ37923	catenin (cadherin-associated protein), beta 1, 88kDa	-	HPRD	12151522
CTNND1	CAS \| CTNND \| KIAA0384 \| P120CAS \| P120CTN \| p120	catenin (cadherin-associated protein), delta 1	-	HPRD	12151522
DLG1	DKFZp761P0818 \| DKFZp781B0426 \| DLGH1 \| SAP97 \| dJ1061C18.1.1 \| hdlg	discs, large homolog 1 (Drosophila)	-	HPRD,BioGRID	11279111
DLG3	KIAA1232 \| MRX \| MRX90 \| NE-Dlg \| NEDLG \| SAP102	discs, large homolog 3 (neuroendocrine-dlg, Drosophila)	-	HPRD	12070168
DLG3	KIAA1232 \| MRX \| MRX90 \| NE-Dlg \| NEDLG \| SAP102	discs, large homolog 3 (neuroendocrine-dlg, Drosophila)	Affinity Capture-Western	BioGRID	9808460
DLG4	FLJ97752 \| FLJ98574 \| PSD95 \| SAP90	discs, large homolog 4 (Drosophila)	-	HPRD	9808460 \|11276111 \|12597860
DLG4	FLJ97752 \| FLJ98574 \| PSD95 \| SAP90	discs, large homolog 4 (Drosophila)	Affinity Capture-Western Reconstituted Complex	BioGRID	9808460 \|11279111 \|12597860
GRIA1	GLUH1 \| GLUR1 \| GLURA \| HBGR1 \| MGC133252	glutamate receptor, ionotropic, AMPA 1	Affinity Capture-Western	BioGRID	8288598
GRIA1	GLUH1 \| GLUR1 \| GLURA \| HBGR1 \| MGC133252	glutamate receptor, ionotropic, AMPA 1	-	HPRD	10358037
GRIA2	GLUR2 \| GLURB \| GluR-K2 \| HBGR2	glutamate receptor, ionotropic, AMPA 2	Affinity Capture-Western	BioGRID	8288598
GRID2	MGC117022 \| MGC117023 \| MGC117024	glutamate receptor, ionotropic, delta 2	Affinity Capture-Western	BioGRID	12573530
GRID2	MGC117022 \| MGC117023 \| MGC117024	glutamate receptor, ionotropic, delta 2	GluR6 interacts with GluR-delta-2	BIND	12573530
GRIK4	EAA1 \| GRIK \| KA1	glutamate receptor, ionotropic, kainate 4	-	HPRD	8288598 \|12954862
GRIK5	EAA2 \| GRIK2 \| KA2	glutamate receptor, ionotropic, kainate 5	-	HPRD,BioGRID	9466455
GRIP1	GRIP	glutamate receptor interacting protein 1	Reconstituted Complex	BioGRID	11891216 \|12597860
PICK1	MGC15204 \| PICK \| PRKCABP	protein interacting with PRKCA 1	-	HPRD,BioGRID	12597860
SDCBP	MDA-9 \| ST1 \| SYCL \| TACIP18	syndecan binding protein (syntenin)	-	HPRD,BioGRID	12597860

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
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 ACTIVATION OF KAINATE RECEPTORS UPON GLUTAMATE BINDING	31	23	All SZGR 2.0 genes in this pathway
REACTOME IONOTROPIC ACTIVITY OF KAINATE RECEPTORS	11	11	All SZGR 2.0 genes in this pathway
ODONNELL TFRC TARGETS UP	456	228	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE FIMA UP	544	308	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP	1278	748	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 24HR DN	148	102	All SZGR 2.0 genes in this pathway
ULE SPLICING VIA NOVA2	43	38	All SZGR 2.0 genes in this pathway
BAELDE DIABETIC NEPHROPATHY DN	434	302	All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR UP	430	288	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER WITH H3K27ME3 DN	228	114	All SZGR 2.0 genes in this pathway
ACEVEDO METHYLATED IN LIVER CANCER DN	940	425	All SZGR 2.0 genes in this pathway
LABBE TGFB1 TARGETS UP	102	64	All SZGR 2.0 genes in this pathway
NUTT GBM VS AO GLIOMA DN	45	22	All SZGR 2.0 genes in this pathway
YAGI AML WITH 11Q23 REARRANGED	351	238	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2	491	319	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 4HR UP	55	41	All SZGR 2.0 genes in this pathway
HOELZEL NF1 TARGETS UP	139	93	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE EARLY LATE	317	190	All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY	1725	838	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
let-7/98	105	111	1A	hsa-let-7a^brain	UGAGGUAGUAGGUUGUAUAGUU
				hsa-let-7b^brain	UGAGGUAGUAGGUUGUGUGGUU
				hsa-let-7c^brain	UGAGGUAGUAGGUUGUAUGGUU
				hsa-let-7d^brain	AGAGGUAGUAGGUUGCAUAGU
				hsa-let-7e^brain	UGAGGUAGGAGGUUGUAUAGU
				hsa-let-7f^brain	UGAGGUAGUAGAUUGUAUAGUU
				hsa-miR-98^brain	UGAGGUAGUAAGUUGUAUUGUU
				hsa-let-7g^SZ	UGAGGUAGUAGUUUGUACAGU
				hsa-let-7i^brain	UGAGGUAGUAGUUUGUGCUGU
miR-153	77	83	1A	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-181	246	252	m8	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-217	282	288	m8	hsa-miR-217	UACUGCAUCAGGAACUGAUUGGAU
miR-218	21	28	1A,m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-363	87	93	1A	hsa-miR-363	AUUGCACGGUAUCCAUCUGUAA
miR-376	122	129	1A,m8	hsa-miR-376a	AUCAUAGAGGAAAAUCCACGU
miR-376	122	129	1A,m8	hsa-miR-376b	AUCAUAGAGGAAAAUCCAUGUU
miR-448	76	83	1A,m8	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-494	61	67	m8	hsa-miR-494^brain	UGAAACAUACACGGGAAACCUCUU
miR-543	59	65	m8	hsa-miR-543	AAACAUUCGCGGUGCACUUCU
miR-543	59	65	m8	hsa-miR-543	AAACAUUCGCGGUGCACUUCU

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: GRIK2