SZGR2

Summary ?

GeneID	2562
Symbol	GABRB3
Synonyms	ECA5
Description	gamma-aminobutyric acid type A receptor beta3 subunit
Reference	MIM:137192\|HGNC:HGNC:4083\|Ensembl:ENSG00000166206\|HPRD:08844\|Vega:OTTHUMG00000129231
Gene type	protein-coding
Map location	15q12
Pascal p-value	5.533E-4
Sherlock p-value	0.617
Fetal beta	-0.705
DMG	1 (# studies)
eGene	Myers' cis & trans
Support	LIGAND GATED ION SIGNALING Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CNV:YES	Copy number variation studies	Manual curation
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGCnp	Genome-wide Association Study	GWAS
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).	1
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
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: 4

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg13904560	15	26870826	GABRB3	1.18E-6	0.583	0.007	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs1155107	chr3	26843376	GABRB3	2562	0.1	trans
rs17029291	chr3	32402138	GABRB3	2562	0.02	trans
rs750544	chr5	51749054	GABRB3	2562	0.14	trans
rs240410	chr6	75940738	GABRB3	2562	0.18	trans
rs418485	chr6	75966268	GABRB3	2562	0.18	trans
rs240388	chr6	75972698	GABRB3	2562	0.18	trans
rs1324669	chr13	107872446	GABRB3	2562	0.01	trans
rs17145698	chrX	40218345	GABRB3	2562	0.03	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.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0030594	neurotransmitter receptor activity	IEA	Neurotransmitter (GO term level: 5)	-
GO:0004890	GABA-A receptor activity	IEA	GABA (GO term level: 7)	-
GO:0004890	GABA-A receptor activity	TAS	GABA (GO term level: 7)	1664410
GO:0005254	chloride channel activity	IEA		-
GO:0005216	ion channel activity	IEA		-
GO:0005230	extracellular ligand-gated ion channel activity	IEA		-
GO:0031404	chloride ion binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007165	signal transduction	TAS		1664410
GO:0006811	ion transport	IEA		-
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:0016021	integral to membrane	IEA		-
GO:0005886	plasma membrane	IEA		-
GO:0005887	integral to plasma membrane	TAS		1664410
GO:0030054	cell junction	IEA		-

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 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES	413	270	All SZGR 2.0 genes in this pathway
REACTOME GABA A RECEPTOR ACTIVATION	12	12	All SZGR 2.0 genes in this pathway
REACTOME GABA RECEPTOR ACTIVATION	52	40	All SZGR 2.0 genes in this pathway
REACTOME ION CHANNEL TRANSPORT	55	42	All SZGR 2.0 genes in this pathway
REACTOME LIGAND GATED ION CHANNEL TRANSPORT	21	21	All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY DN	367	220	All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS DN	536	332	All SZGR 2.0 genes in this pathway
ODONNELL METASTASIS UP	82	58	All SZGR 2.0 genes in this pathway
HUMMERICH SKIN CANCER PROGRESSION UP	88	58	All SZGR 2.0 genes in this pathway
BENPORATH ES 1	379	235	All SZGR 2.0 genes in this pathway
POMEROY MEDULLOBLASTOMA DESMOPLASIC VS CLASSIC UP	62	38	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
KAAB HEART ATRIUM VS VENTRICLE UP	249	170	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT DN	165	106	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS UP	170	107	All SZGR 2.0 genes in this pathway
EHLERS ANEUPLOIDY DN	12	8	All SZGR 2.0 genes in this pathway
CONRAD STEM CELL	39	27	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR DN	36	19	All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 AND SATB1 DN	180	116	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
miR-128	2301	2307	1A	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
miR-128	2301	2307	1A	hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-194	2904	2910	m8	hsa-miR-194	UGUAACAGCAACUCCAUGUGGA
miR-203.1	2670	2676	1A	hsa-miR-203	UGAAAUGUUUAGGACCACUAG
miR-204/211	329	335	m8	hsa-miR-204^brain	UUCCCUUUGUCAUCCUAUGCCU
miR-204/211	329	335	m8	hsa-miR-211	UUCCCUUUGUCAUCCUUCGCCU
miR-218	4121	4127	m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-218	4121	4127	m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-23	136	142	1A	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
miR-23	136	142	1A	hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-26	1798	1804	m8	hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
miR-26	1798	1804	m8	hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
miR-27	2301	2307	m8	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	2301	2307	m8	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-369-3p	4144	4150	m8	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-383	1362	1368	m8	hsa-miR-383^brain	AGAUCAGAAGGUGAUUGUGGCU
miR-421	1312	1318	1A	hsa-miR-421	GGCCUCAUUAAAUGUUUGUUG
miR-431	1411	1417	1A	hsa-miR-431	UGUCUUGCAGGCCGUCAUGCA
miR-448	2479	2485	m8	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-455	3486	3492	m8	hsa-miR-455	UAUGUGCCUUUGGACUACAUCG
miR-485-5p	1371	1378	1A,m8	hsa-miR-485-5p	AGAGGCUGGCCGUGAUGAAUUC
miR-486	4021	4028	1A,m8	hsa-miR-486	UCCUGUACUGAGCUGCCCCGAG
miR-488	1987	1993	1A	hsa-miR-488	CCCAGAUAAUGGCACUCUCAA
miR-500	1418	1424	m8	hsa-miR-500	AUGCACCUGGGCAAGGAUUCUG
miR-539	144	150	1A	hsa-miR-539	GGAGAAAUUAUCCUUGGUGUGU
miR-542-3p	1566	1572	1A	hsa-miR-542-3p	UGUGACAGAUUGAUAACUGAAA

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: GABRB3