Table 5.
Pathway enrichment analyses for Gene Ontology (GO), KEGG, and Pathway Commons (PC) (separate pathways with BH-corrected p value < 0.1) based on significant findings from EWAS for level of lung function
| Lung function measure | Database | Pathway name | No. of genes | Genes | Statistics |
|---|---|---|---|---|---|
| Log-ΔzFEV1IP | GO | Negative regulation of BMP signaling pathway | 2 | BMPER SKI | C = 32; O = 2; E = 0.01; R = 142.86; rawP = 7.87e-05; adjP = 0.0114 |
| Ubiquitin protein ligase binding | 2 | DAXX SKI | C = 147; O = 2; E = 0.05; R = 38.69; rawP = 0.0010; adjP = 0.0090 | ||
| PML body | 2 | DAXX SKI | C = 72; O = 2; E = 0.02; R = 87.37; rawP = 0.0002; adjP = 0.0052 | ||
| PC | TGFBR | 2 | DAXX SKI | C = 125; O = 2; E = 0.05; R = 43.92; rawP = 0.0009; adjP = 0.0450 | |
| Log-ΔzFVCIP | No significant pathway enrichment results | ||||
| ΔzFEV1/FVCIP | GO | Protein homodimerization activity | 3 | MTHFD1L ANXA9 PRKRA | C = 554; O = 3; E = 0.27; R = 11.00; rawP = 0.0018; adjP = 0.0324 |
| KEGG | Metabolic pathways | 2 | ADH6 MTHFD1L | C = 1093; O = 2; E = 0.46; R = 4.39; rawP = 0.0720; adjP = 0.0720 | |
Bold indicates BH adjP < 0.05
C the number of reference genes in the category, O the number of genes in the gene set and also in the category, E the expected number in the category, R ratio of enrichment, rawP p value from hypergeometric test, adjP p value adjusted by the multiple test adjustment (BH)