Summary ?
GeneID1135
SymbolCHRNA2
Synonyms-
Descriptioncholinergic receptor nicotinic alpha 2 subunit
ReferenceMIM:118502|HGNC:HGNC:1956|Ensembl:ENSG00000120903|HPRD:00332|Vega:OTTHUMG00000102083
Gene typeprotein-coding
Map location8p21
Pascal p-value0.004
DMG1 (# studies)
eGeneCerebellar Hemisphere
Cerebellum

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
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). 1
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
GSMA_IGenome scan meta-analysisPsr: 0.031 
GSMA_IIEGenome scan meta-analysis (European-ancestry samples)Psr: 0.00057 
GSMA_IIAGenome scan meta-analysis (All samples)Psr: 0.03086 
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: 3 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg15744111827336890CHRNA27.82E-5-0.3890.025DMG:Wockner_2014


Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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
AC005544.10.860.85
CACNG40.860.86
FGD10.850.88
CUL70.840.86
HCN30.840.88
IFT1400.840.85
PLEKHG4B0.840.86
REC80.830.85
UBAP20.830.85
C17orf700.830.84
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
C5orf53-0.65-0.76
HLA-F-0.64-0.74
AIFM3-0.62-0.72
S100B-0.62-0.78
CA4-0.62-0.72
ALDOC-0.62-0.67
AF347015.27-0.61-0.80
AF347015.31-0.61-0.79
PTH1R-0.61-0.69
CSRP1-0.61-0.72

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0015464acetylcholine receptor activityIDANeurotransmitter (GO term level: 6)8906617 
GO:0004889nicotinic acetylcholine-activated cation-selective channel activityIDA8906617 
GO:0005216ion channel activityIEA-
GO:0005230extracellular ligand-gated ion channel activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007165signal transductionIDA8906617 
GO:0006811ion transportNAS8906617 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005892nicotinic acetylcholine-gated receptor-channel complexIDANeurotransmitter (GO term level: 9)8906617 
GO:0045211postsynaptic membraneIEASynap, Neurotransmitter (GO term level: 5)-
GO:0045202synapseIEAneuron, Synap, Neurotransmitter, Glial (GO term level: 2)-
GO:0016021integral to membraneNAS8906617 
GO:0005886plasma membraneIEA-
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
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 ACETYLCHOLINE BINDING AND DOWNSTREAM EVENTS 1613All SZGR 2.0 genes in this pathway
REACTOME HIGHLY CALCIUM PERMEABLE POSTSYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 1312All SZGR 2.0 genes in this pathway
REACTOME PRESYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 1210All SZGR 2.0 genes in this pathway
MCCABE BOUND BY HOXC6 469239All SZGR 2.0 genes in this pathway
MCCABE HOXC6 TARGETS UP 108All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305895All SZGR 2.0 genes in this pathway
YAGI AML WITH 11Q23 REARRANGED 351238All SZGR 2.0 genes in this pathway
RATTENBACHER BOUND BY CELF1 467251All SZGR 2.0 genes in this pathway