Table 4.
Results of rare/low-frequency variants analysis: a list of the most significantly enriched pathways (P value < 0.05) from gene set enrichment analysis using WebGestalt.
| Accession | Pathway name | P value | Adjusted P value* |
|---|---|---|---|
| Gene ontology biological process | |||
| GO:1903828 | Negative regulation of cellular protein localization | 4.40E−02 | 6.42E−01 |
| GO:0002263 | Cell activation involved in immune response | 3.90E−02 | 6.43E−01 |
| GO:0044706 | Multi-multicellular organism process | 2.60E−02 | 6.50E−01 |
| Gene ontology cellular localization | |||
| GO:0005790 | Smooth endoplasmic reticulum | 5.02E−03 | 4.70E−02 |
| GO:0042579 | Microbody | 8.00E−03 | 4.46E−01 |
| GO:0044815 | DNA packaging complex | 4.60E−02 | 4.70E−01 |
| GO:0005793 | Endoplasmic reticulum-Golgi intermediate compartment | 8.00E−03 | 4.80E−01 |
| GO:0031225 | Anchored component of membrane | 2.80E−02 | 4.94E−01 |
| GO:0031201 | SNARE complex | 2.90E−02 | 5.10E−01 |
| GO:0048770 | Pigment granule | 1.50E−02 | 5.75E−01 |
| GO:0044306 | Neuron projection terminus | 4.20E−02 | 5.88E−01 |
| Gene ontology molecular function | |||
| GO:0000149 | SNARE binding | 2.00E−03 | 6.77E−01 |
| GO:0016776 | Phosphotransferase activity, phosphate group as acceptor | 1.61E−02 | 7.26E−01 |
| GO:0001085 | RNA polymerase II transcription factor binding | 1.00E−02 | 7.69E−01 |
| KEGG | |||
| hsa00760 | Nicotinate and nicotinamide metabolism: Homo sapiens | 1.01E−02 | 3.73E−01 |
| PANTHER | |||
| P04378 | Beta2 adrenergic receptor signaling pathway | 4.24E−02 | 2.69E−01 |
| P05912 | Dopamine receptor mediated signaling pathway | 1.11E−02 | 3.00E−01 |
| P00053 | T cell activation | 1.70E−02 | 3.48E−01 |
| P00047 | PDGF signaling pathway | 2.80E−02 | 5.16E−01 |
| Reactome | |||
| R-HSA-2151201 | Transcriptional activation of mitochondrial biogenesis | 3.01E−03 | 4.67E−01 |
| R-HSA-179419 | APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint | 2.11E−02 | 5.70E−01 |
| R-HSA-453276 | Regulation of mitotic cell cycle | 1.40E−02 | 5.74E−01 |
| R-HSA-2262752 | Cellular responses to stress | 2.50E−02 | 5.76E−01 |
| Wikipathways | |||
| WP481 | Insulin signaling | 1.90E−02 | 7.74E−01 |
| WP455 | GPCRs, Class A Rhodopsin-like | 8.00E−03 | 7.81E−01 |
SNARE soluble N-ethylmaleimide-sensitive factor attachment protein receptor, PDGF platelet-derived growth factor, APC/C anaphase-promoting complex, GPCR G-protein-coupled receptor.
*By Benjamini–Hochberg procedure.
Numbers in bold indicate the smallest adjusted p-values, i.e. most significant pathway enrichments among all rows in the table.