Gene Page:PCDHB6
Summary?
| GeneID | 56130 |
| Symbol | PCDHB6 |
| Synonyms | PCDH-BETA6 |
| Description | protocadherin beta 6 |
| Reference | MIM:606332|HGNC:HGNC:8691|Ensembl:ENSG00000113211|HPRD: 07561|Vega:OTTHUMG00000129623 |
| Gene type | protein-coding |
| Map location | 5q31 |
| Pascal p-value | 0.012 |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| GSMA_I | Genome scan meta-analysis | Psr: 0.0032 | |
| GO_Annotation | Mapping neuro-related keywords to Gene Ontology annotations | Hits with neuro-related keywords: 2 |
Section I. Genetics and epigenetics annotation
Section II. Transcriptome annotation
General gene expression (GTEx)
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 |
| MYO16 | 0.79 | 0.83 |
| NFE2L3 | 0.78 | 0.79 |
| GNAZ | 0.74 | 0.78 |
| AC079061.1 | 0.74 | 0.74 |
| WWC1 | 0.74 | 0.72 |
| IL27RA | 0.74 | 0.77 |
| PPP1R14C | 0.73 | 0.73 |
| PIK3R2 | 0.73 | 0.82 |
| AC132186.2 | 0.72 | 0.72 |
| GPRIN1 | 0.72 | 0.83 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| AF347015.27 | -0.50 | -0.68 |
| AIFM3 | -0.50 | -0.63 |
| CSRP1 | -0.49 | -0.64 |
| AIF1L | -0.49 | -0.65 |
| TSC22D4 | -0.49 | -0.63 |
| AF347015.33 | -0.49 | -0.67 |
| PIR | -0.49 | -0.65 |
| AF347015.31 | -0.49 | -0.67 |
| S100A1 | -0.48 | -0.70 |
| HLA-F | -0.48 | -0.61 |
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0005509 | calcium ion binding | IEA | - | |
| GO:0005515 | protein binding | NAS | 11322959 | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0007416 | synaptogenesis | TAS | Synap (GO term level: 6) | 12231349 |
| GO:0007268 | synaptic transmission | TAS | neuron, Synap, Neurotransmitter (GO term level: 6) | 12231349 |
| GO:0007155 | cell adhesion | TAS | 10380929 | |
| GO:0007156 | homophilic cell adhesion | IEA | - | |
| GO:0016339 | calcium-dependent cell-cell adhesion | NAS | 11322959 | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0005886 | plasma membrane | IEA | - | |
| GO:0005887 | integral to plasma membrane | TAS | 10380929 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| ODONNELL METASTASIS UP | 82 | 58 | All SZGR 2.0 genes in this pathway |
| KOYAMA SEMA3B TARGETS UP | 292 | 168 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN ES ICP WITH H3K27ME3 | 42 | 27 | All SZGR 2.0 genes in this pathway |