Gene Page: GABRG3
Summary ?
| GeneID | 2567 |
| Symbol | GABRG3 |
| Synonyms | - |
| Description | gamma-aminobutyric acid type A receptor gamma3 subunit |
| Reference | MIM:600233|HGNC:HGNC:4088|Ensembl:ENSG00000182256|HPRD:02579|Vega:OTTHUMG00000044462 |
| Gene type | protein-coding |
| Map location | 15q12 |
| Pascal p-value | 0.909 |
| Fetal beta | -0.577 |
| DMG | 1 (# studies) |
| Support | 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: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). | 3 |
| 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: 5 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg19816354 | 15 | 27519506 | GABRG3 | 2.82E-5 | -0.355 | 0.018 | DMG:Wockner_2014 |
| cg02769599 | 15 | 27503580 | GABRG3 | 4.41E-5 | -0.391 | 0.021 | DMG:Wockner_2014 |
| cg19843449 | 15 | 27217186 | GABRG3 | 1.786E-4 | 0.399 | 0.034 | DMG:Wockner_2014 |
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 |
| ASB6 | 0.92 | 0.91 |
| ZFYVE27 | 0.92 | 0.91 |
| RNF123 | 0.90 | 0.90 |
| TBC1D25 | 0.90 | 0.89 |
| RPS6KL1 | 0.89 | 0.90 |
| MBD1 | 0.89 | 0.89 |
| RMND5B | 0.88 | 0.86 |
| AGPAT1 | 0.88 | 0.89 |
| COG8 | 0.88 | 0.87 |
| APBA2 | 0.88 | 0.88 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| AF347015.31 | -0.74 | -0.68 |
| AF347015.21 | -0.74 | -0.74 |
| MT-CO2 | -0.73 | -0.67 |
| AF347015.8 | -0.73 | -0.68 |
| AL139819.3 | -0.73 | -0.76 |
| MT-CYB | -0.72 | -0.65 |
| AF347015.2 | -0.71 | -0.62 |
| AF347015.26 | -0.70 | -0.63 |
| AF347015.33 | -0.70 | -0.64 |
| AF347015.27 | -0.70 | -0.68 |
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:0005254 | chloride channel activity | IEA | - | |
| GO:0005216 | ion channel activity | IEA | - | |
| GO:0005230 | extracellular ligand-gated ion channel activity | NAS | - | |
| GO:0031404 | chloride ion binding | IEA | - | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0007268 | synaptic transmission | NAS | neuron, Synap, Neurotransmitter (GO term level: 6) | - |
| GO:0007214 | gamma-aminobutyric acid signaling pathway | IEA | GABA, Neurotransmitter (GO term level: 8) | - |
| GO:0006821 | chloride transport | IEA | - | |
| 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 | NAS | - | |
| GO:0005886 | plasma membrane | IEA | - | |
| 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 |
| DELYS THYROID CANCER UP | 443 | 294 | All SZGR 2.0 genes in this pathway |
| BENPORATH ES WITH H3K27ME3 | 1118 | 744 | All SZGR 2.0 genes in this pathway |
| XU CREBBP TARGETS DN | 44 | 31 | All SZGR 2.0 genes in this pathway |
| YOSHIMURA MAPK8 TARGETS UP | 1305 | 895 | All SZGR 2.0 genes in this pathway |
| MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3 | 349 | 234 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN NPC HCP WITH H3K27ME3 | 341 | 243 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN MEF HCP WITH H3K27ME3 | 590 | 403 | All SZGR 2.0 genes in this pathway |