Table 2.
Most significant associations identified in the integrative gene set analysis
| Gene Ontology annotation | DMR | RNA | Prot | FDR | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| N | FC | P-value | N | FC | P-value | N | FC | P-value | ||
| Extracellular matrix organization* | 30 | 1.71 | 0.0026 | 40 | 1.48 | 0.0049 | 22 | 1.90 | 0.0072 | 0.0034 |
| Gluconeogenesis | 4 | 0.98 | 0.71 | 7 | 1.13 | 0.52 | 19 | 3.90 | 0.00001 | 0.0034 |
| Positive regulation of cytosolic calcium ion concentration | 11 | 1.44 | 0.081 | 20 | 2.45 | 0.00001 | 3 | 1.85 | 0.24 | 0.0034 |
| Skeletal system development* | 22 | 2.02 | 0.0012 | 28 | 1.53 | 0.0028 | 12 | 2.27 | 0.002 | 0.0034 |
| Inflammatory response | 19 | 1.07 | 0.40 | 44 | 1.89 | 0.00001 | 8 | 1.09 | 0.43 | 0.0081 |
| Endodermal cell differentiation* | 9 | 2.55 | 0.0054 | 12 | 2.14 | 0.0056 | 6 | 2.11 | 0.036 | 0.011 |
| Positive regulation of ERK1 and ERK2 cascade* | 19 | 1.60 | 0.014 | 21 | 1.53 | 0.013 | 11 | 2.17 | 0.0042 | 0.012 |
| Positive regulation of peptidyl-tyrosine phosphorylation | 10 | 1.61 | 0.079 | 18 | 1.94 | 0.0017 | 7 | 2.46 | 0.0032 | 0.012 |
| Collagen catabolic process | 16 | 2.27 | 0.0024 | 12 | 1.15 | 0.32 | 13 | 2.46 | 0.0013 | 0.012 |
| Platelet aggregation* | 8 | 1.95 | 0.048 | 12 | 1.71 | 0.027 | 11 | 2.71 | 0.002 | 0.016 |
All shown Gene Ontology terms are enriched in the cross-omics analysis at below 2% FDR. DMR: differentially methylated region; RNA: gene expression; Prot: protein abundance; N: number of significant genes annotated to GO term; FC: fold-change enrichment; P: within-omics empirical P-values for enrichment. FDR: integrative false-discovery rate based on combination of the three-omics P-values (see Methods section).
*
The terms with enrichment P < 0.05 across all individual omics analyses.