Figure 3

Hierarchical clustering of cross-species and species-specific hybridization data corresponding to cross-species matched probe sets. Hierarchical clustering of biological replicates by using Centered Pearson correlation, applied to (nematode-) infected:non-infected (potato plants) ratios of (A) The whole System Expression Matrix (SEM), comprising PP and PT data of 17,325 potato-tomato pairs with homology level of E-value ≤ e-1. (B) A subset of SEM, corresponding to 7,116 pairs with homology level of bit-scores ≥ 129 (or E-values ≤ e-26). The first letter of a condition name designates the RNA source ('P' for potato plants); the second letter indicates the microarray chip platform ('P' or 'T' for TIGR potato or CGEP tomato microarray chip, respectively); '10' or '5' designates days of nematode infection; 'a' or 'b' designates biological replicates. Color scale represents gene expression fold change.