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Table 1 Temperature and hypoxia treatment effects on the extracted scores of the first two principal components

From: The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

Linear Mixed-Effect Models For Each Principal Component (PC-1 and PC-2)a
Microarrayb PC Var % Factors Num DF Den DF F-value p-value CT vs WN CT vs WH WN vs WH
All Probes (17,072) PC-1 16.6 Intercept 1 12 20.6 7e-4    
Treatment 2 3 384.6 2e-4 2e-4 0.001 0.489
PC-2 10.4 Intercept 1 12 0.4 0.531    
Treatment 2 3 1.0 0.477    
DEPs WN & WH (1111) PC-1 61.5 Intercept 1 12 19.1 9e-4    
Treatment 2 3 687.6 1e-4 < 0.0001 2e-4 0.841
PC-2 4.6 Intercept 1 12 0.3 0.623    
Treatment 2 3 1.0 0.470    
DEPs WN (789) PC-1 46.6 Intercept 1 12 819.3 < 0.0001    
Treatment 2 3 506.0 2e-4 6e-4 2e-4 0.012
PC-2 6.3 Intercept 1 12 1.8 0.209    
Treatment 2 3 0.9 0.506    
DEPs WH (994) PC-1 42.1 Intercept 1 12 252.3 < 0.0001    
Treatment 2 3 875.0 1e-4 0.002 < 0.0001 0.007
PC-2 7.7 Intercept 1 12 0.6 0.441    
Treatment 2 3 0.0 0.982    
qPCRc           
All Target Genes (41) PC-1 39.4 Intercept 1 18 147.5 < 0.0001    
Treatment 2 3 318.4 3e-4 3e-4 6e-4 0.747
PC-2 18.2 Intercept 1 18 46.9 < 0.0001    
Treatment 2 3 1.2 0.416    
Stress-Related Genes (24) PC-1 45.9 Intercept 1 18 713.9 < 0.0001    
Treatment 2 3 488.3 2e-4 1e-4 2e-4 0.537
PC-2 19.6 Intercept 1 18 16.9 7e-4    
Treatment 2 3 1.2 0.423    
Immune-Related Genes (14) PC-1 30.7 Intercept 1 18 1.5 0.237    
Treatment 2 3 32.8 0.009 0.011 0.012 0.405
PC-2 23.6 Intercept 1 18 0.0 0.870    
Treatment 2 3 1.2 0.417    
  1. a Linear mixed-effect models (LMEs) were performed for the first two principal components (PC-1 and PC-2) individually to assess the effect of the fixed factor ‘treatment’ and included the random term ‘tank’. The variance explained by each PC is indicated in percentage (%) values. For the pairwise comparisons between the Control (CT), Warm & Normoxic (WN) and Warm & Hypoxic (WH) treatment groups, lsmeans post-hoc tests with Tukey’s multiple comparisons adjustment of p-values were applied. Significant p-values are marked in bold letters (p < 0.05)
  2. b Statistical approach based on normalized log2 ratios of 17,072 detected microarray probes, 1111 WN & WH-specific differentially expressed probes (DEPs), 789 WN-specific DEPs and 994 WH-specific DEPs
  3. c Statistical approach based on the relative expression values (RQ) of 41 target genes, 24 stress-related genes and 14 immune-related genes measured with qPCR (Fluidigm Biomark™) (see Table 2)