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Table 3 Comparison of Hallmark gene sets identified in whole-genome transcriptome data between COPD (n = 19) and Healthy (n = 34), assessed at baseline and as resistance training-associated changes

From: Chronic obstructive pulmonary disease does not impair responses to resistance training

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)
  1. *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