Comparison
|
Gene set
|
Significance category*
|
Set size†
|
Rank P-value‡
|
% MSD > 0§
|
GSEA P-value||
|
NES
|
LE**
|
Log2 fold difference in LE (95% CI)
|
---|
Baseline: COPD vs Healthy
|
Oxidative phosphorylation
|
Consensus
|
190 (200)
|
0.007
|
36.8%
|
< 0.001
|
− 2.10
|
70 (94.3%)
|
− 0.24 (− 0.45, − 0.13)
|
Myogenesis
|
Rank
|
163 (200)
|
< 0.001
|
33.7%
|
0.417
|
1.21
|
45 (75.6%)
|
0.46 (0.19, 1.5)
|
3½ weeks of training: ΔCOPD vs ΔHealthy
|
Allograft rejection
|
GSEA
|
115 (200)
|
0.956
|
7.8%
|
0.014
|
1.71
|
20 (35%)
|
0.39 (0.13, 0.76)
|
Oxidative phosphorylation
|
GSEA
|
190 (200)
|
0.999
|
1.1%
|
0.009
|
1.69
|
83 (2.4%)
|
0.11 (0.05, 0.39)
|
Pancreas beta cells
|
GSEA
|
15 (40)
|
0.969
|
6.7%
|
0.028
|
1.71
|
3 (33.3%)
|
0.35 (0.08, 0.54)
|
Post− RT (13 weeks of training): ΔCOPD vs ΔHealthy
|
Myogenesis
|
Consensus
|
163 (200)
|
< 0.001
|
42.3%
|
< 0.001
|
− 1.52
|
68 (85.3%)
|
− 0.5 (− 1.13, − 0.26)
|
- *Consensus significance indicates agreement between directional (GSEA) and non-directional (Rank) hypothesis test of overrepresentation (see methods for details). †Indicates number of identified genes in the gene set and total number of genes in the gene set in parentheses. ‡Rank-based enrichment test, based on minimum significant difference (MSD), identifies gene sets that are overrepresented among top-ranked genes without a directional hypothesis. § Fraction of genes in gene set with unadjusted 95% CI not spanning zero, i.e. MSD > 0. || Gene-set enrichment analysis (GSEA) tests for overrepresentation among top and bottom genes based on Log2 fold differences or changes × -log10(P-values) in comparing differences at baseline or changes from baseline between COPD and Healthy. A positive normalized enrichment score (NES) indicate gene set with higher expression in COPD than Healthy; negative NES indicate gene set with lower expression at respective time-points. ** Number of genes in leading edge (LE, genes that contributes to the enrichment score) with the fraction of leading edge genes with unadjusted 95% CI not spanning zero. ∆ change score