Gene Page: GABRA1

Summary ?
GeneID2554
SymbolGABRA1
SynonymsECA4|EIEE19|EJM|EJM5
Descriptiongamma-aminobutyric acid type A receptor alpha1 subunit
ReferenceMIM:137160|HGNC:HGNC:4075|Ensembl:ENSG00000022355|HPRD:00662|Vega:OTTHUMG00000163586
Gene typeprotein-coding
Map location5q34
Pascal p-value0.01
Sherlock p-value0.843
Fetal beta-4.369
DMG2 (# studies)
SupportLIGAND GATED ION SIGNALING
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS
CompositeSet

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
ADT:Sun_2012Systematic Investigation of Antipsychotic Drugs and Their TargetsA total of 382 drug-target associations involving 43 antipsychotic drugs and 49 target genes.
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis 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_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 2
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
AssociationA combined odds ratio method (Sun et al. 2008), association studies2Link to SZGene
GSMA_IGenome scan meta-analysisPsr: 0.0032 
GSMA_IIEGenome scan meta-analysis (European-ancestry samples)Psr: 0.01718 
GSMA_IIAGenome scan meta-analysis (All samples)Psr: 0.00459 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 4 
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.3066 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg024691865161277234GABRA13.18E-40.4590.04DMG:Wockner_2014
cg020653875161274307GABRA14.18E-8-0.0341.17E-5DMG:Jaffe_2016


Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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
GenePearson's Correlation Spearman's Correlation
NEB0.410.40
CCDC1360.400.35
CACNA1G0.390.33
CAPRIN20.390.39
DQX10.380.27
GRM10.380.36
GBA20.380.41
FBXO100.370.41
IL21R0.370.21
TMEM41A0.370.28
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
GNG11-0.27-0.34
PRKCDBP-0.25-0.25
CLEC3B-0.25-0.29
METRN-0.24-0.24
MYL12A-0.24-0.27
AL138743.2-0.24-0.25
CCDC72-0.23-0.30
VAMP5-0.23-0.25
RPL35-0.23-0.25
IGFBP7-0.23-0.25

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0030594neurotransmitter receptor activityIEANeurotransmitter (GO term level: 5)-
GO:0004890GABA-A receptor activityTASGABA (GO term level: 7)2465923 
GO:0005515protein bindingIEA-
GO:0005254chloride channel activityIEA-
GO:0005216ion channel activityIEA-
GO:0005230extracellular ligand-gated ion channel activityIEA-
GO:0031404chloride ion bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007214gamma-aminobutyric acid signaling pathwayTASGABA, Neurotransmitter (GO term level: 8)2465923 
GO:0006821chloride transportIEA-
GO:0006811ion transportIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0045211postsynaptic membraneIEASynap, Neurotransmitter (GO term level: 5)-
GO:0045202synapseIEAneuron, Synap, Neurotransmitter, Glial (GO term level: 2)-
GO:0005886plasma membraneIEA-
GO:0005887integral to plasma membraneTAS2465923 
GO:0030054cell junctionIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION 272195All SZGR 2.0 genes in this pathway
BIOCARTA GABA PATHWAY 1010All SZGR 2.0 genes in this pathway
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES 186155All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM 279221All SZGR 2.0 genes in this pathway
REACTOME NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 137110All SZGR 2.0 genes in this pathway
REACTOME TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 413270All SZGR 2.0 genes in this pathway
REACTOME GABA A RECEPTOR ACTIVATION 1212All SZGR 2.0 genes in this pathway
REACTOME GABA RECEPTOR ACTIVATION 5240All SZGR 2.0 genes in this pathway
REACTOME ION CHANNEL TRANSPORT 5542All SZGR 2.0 genes in this pathway
REACTOME LIGAND GATED ION CHANNEL TRANSPORT 2121All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP 485293All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM4 261153All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN 428306All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS DN 357212All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST UP 398262All SZGR 2.0 genes in this pathway
MATSUDA NATURAL KILLER DIFFERENTIATION 475313All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR DN 504323All SZGR 2.0 genes in this pathway
MCCLUNG CREB1 TARGETS UP 10072All SZGR 2.0 genes in this pathway
JIANG AGING CEREBRAL CORTEX DN 5443All SZGR 2.0 genes in this pathway
KONDO PROSTATE CANCER WITH H3K27ME3 19693All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS PTEN UP 181112All SZGR 2.0 genes in this pathway
HELLEBREKERS SILENCED DURING TUMOR ANGIOGENESIS 8056All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP 548370All SZGR 2.0 genes in this pathway
PANGAS TUMOR SUPPRESSION BY SMAD1 AND SMAD5 DN 157106All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-137148314891Ahsa-miR-137UAUUGCUUAAGAAUACGCGUAG
miR-14653591Ahsa-miR-146aUGAGAACUGAAUUCCAUGGGUU
hsa-miR-146bbrainUGAGAACUGAAUUCCAUAGGCU
miR-15/16/195/424/497179117971Ahsa-miR-15abrainUAGCAGCACAUAAUGGUUUGUG
hsa-miR-16brainUAGCAGCACGUAAAUAUUGGCG
hsa-miR-15bbrainUAGCAGCACAUCAUGGUUUACA
hsa-miR-195SZUAGCAGCACAGAAAUAUUGGC
hsa-miR-424CAGCAGCAAUUCAUGUUUUGAA
hsa-miR-497CAGCAGCACACUGUGGUUUGU
miR-1819139201A,m8hsa-miR-181abrainAACAUUCAACGCUGUCGGUGAGU
hsa-miR-181bSZAACAUUCAUUGCUGUCGGUGGG
hsa-miR-181cbrainAACAUUCAACCUGUCGGUGAGU
hsa-miR-181dbrainAACAUUCAUUGUUGUCGGUGGGUU
hsa-miR-181abrainAACAUUCAACGCUGUCGGUGAGU
hsa-miR-181bSZAACAUUCAUUGCUGUCGGUGGG
hsa-miR-181cbrainAACAUUCAACCUGUCGGUGAGU
hsa-miR-181dbrainAACAUUCAUUGUUGUCGGUGGGUU
miR-203.1192119281A,m8hsa-miR-203UGAAAUGUUUAGGACCACUAG
miR-21610151021m8hsa-miR-216UAAUCUCAGCUGGCAACUGUG
miR-221/222140114081A,m8hsa-miR-221brainAGCUACAUUGUCUGCUGGGUUUC
hsa-miR-222brainAGCUACAUCUGGCUACUGGGUCUC
miR-3209449501Ahsa-miR-320AAAAGCUGGGUUGAGAGGGCGAA
miR-34b187718831Ahsa-miR-34bUAGGCAGUGUCAUUAGCUGAUUG
miR-376c150415101Ahsa-miR-376cAACAUAGAGGAAAUUCCACG
miR-4109269321Ahsa-miR-410AAUAUAACACAGAUGGCCUGU
miR-493-5p14321438m8hsa-miR-493-5pUUGUACAUGGUAGGCUUUCAUU
miR-49699910051Ahsa-miR-496AUUACAUGGCCAAUCUC
miR-503179117971Ahsa-miR-503UAGCAGCGGGAACAGUUCUGCAG
miR-5059109161Ahsa-miR-505GUCAACACUUGCUGGUUUCCUC