Figure 3. Workflow and results for Mixed Model analysis of HNE dataset.

When individual tests were conducted with 6 hr treatment samples and 24 hr samples separately, only 5 and 1 gene-sets were significant at 0.01 FDR level. However, when all samples were used, for testing gene-sets with non-significant Duration×Linear Trend interaction, 40 gene-sets were significant at 0.01 FDR level. This shows pooling data with similar trends from both treatment durations improves the statistical power for identifying biologically meaningful gene sets.