Table 4 Coding hotspots based on weight of genomic regions and enriched Gene Ontology (GO)/KEGG pathways.
Variation type | Locus | Weight for case–control classifications (%) | Weight for multiple labeling (%) | Num genes contain corresponding variation | Enriched Gene Ontology/pathways (Benjamini–Hochberg adjusted p value) |
|---|---|---|---|---|---|
Stop codon | chr19:1-50000000 | 1.1 | 1.2 | 59 | – |
Stop codon | chr19:50000001-55000000 | 1.5 | 1.5 | 68 | Regulation of immune response (2.2E-4); regulation of transcription (5.1E-4); osteoclast differentiation (2.1E-5); antigen processing and presentation (5.2E-4) |
Stop codon | chr11:55000001-60000000 | 1.2 | 1.2 | 42 | G-protein-coupled receptor signaling pathway (4.3E-27); olfactory receptor activity (2.3E-36); olfactory transduction (1.8E-31) |
Stop codon | chr17:35000001-40000000 | 1.0 | 1.1 | 33 | Lymphocyte/monocyte chemotaxis (2.1E-3); chemokine-mediated signaling pathway (5.3E-3); chemokine signaling pathway (0.034); cytokine-cytokine receptor interaction (0.036) |
Frameshift SNVs | chr11:55000001-60000000 | 1.3 | 1.4 | 49 | G-protein-coupled receptor signaling pathway (4E-30); in sensory perception of smell (2E-42); olfactory receptor activity (1.3E-42); olfactory transduction (9.1E-35) |
Frameshift SNVs | chr16:55000001-60000000 | 1.3 | 1.3 | 27 | – |
Frameshift SNVs | chr19:50000001-55000000 | 1.3 | 1.4 | 76 | IMMUNE category diseases (6.9E-3); regulation of immune response (3.2E-11); regulation of transcription (3.2E-3); receptor activity (8.3E-3); osteoclast differentiation (1.2E-8); antigen processing and presentation (2.9E-6); natural killer cell-mediated cytotoxicity (5.3E-4) |
Frameshift SNVs | chr6:30000001-35000000 | 1.1 | 1.2 | 65 | IMMUNE category diseases (2.5E-29); MHC class II receptor activity (1.2E-3); antigen processing and presentation (4.1E-5) |
Frameshift SNVs | chr7:100000001-105000000 | 1.1 | 1.2 | 33 | – |
