After calculation of normalized expression values for each sample, DE genes after inoculation [false-discovery rate (FDR) ≤ 0.001] were determined for each inoculation treatment using the edgeR software (Robinson et al. 2010). The set of exclusive DE genes in samples inoculated with D. ampelina was obtained by subtracting genes that were DE after both pathogen and mock inoculation. These inoculated-exclusive DE genes were input for pathway enrichment analysis as previously described (Osier 2016). The experiment described in the above section is referred to as a DE study in the following sections.