Figure 4

Principal component analysis (PCA) of subsets of the System Expression Matrix (SEM) of cross-species and species-specific hybridization experiments. PCA of (nematode-) infected:non-infected (potato plants) ratios of (A) The whole System Expression Matrix (SEM), corresponding to 17,325 potato-tomato clone pairs (E value ≤ e-1); (B) A subset of SEM, corresponding to 7,116 potato-tomato clone pairs (bit-scores ≥ 129 or E-values ≤ e-26). PCA was performed across two time-points (5 and 10 d of nematode infection) and two biological replicates (labeled as 'a' or 'b'), resulted from species-specific hybridization (SSH) of potato RNA to potato microarrays (denoted as PP) and from cross-species hybridization of potato RNA to tomato microarrays (denoted as PT). Axes 1, 2 and 3 account for (A) 31.0, 21.3 and 13.8 %, (B) 31.0, 23.0 and 14.6 % of the variation, respectively. Biological replicates are circled.