Table 1.

Description of the four analysis categories and subcategories, and the GeneChip datasets used for each analysis. The first named dataset in each comparison was considered the experimental data, and the second named was the control (baseline) data.

GeneChip datasets compared	Category
Yr5 Pst‐inoculated—mock‐inoculated	1. Incompatible interaction
	a. HR‐specific transcripts
	b. Basal defence transcripts
yr5 Pst‐inoculated—mock‐inoculated	2. Compatible interaction
	a. Basal defence transcripts
	b. Biotrophic interaction‐specific transcripts
Yr5 Pst‐inoculated—yr5 Pst‐inoculated	3. Constitutive Yr5‐controlled transcripts
	a.  Pst‐specific Yr5 transcripts
	b.  Pst‐specific yr5 transcripts
	c. Incomplete isogenicity transcripts
Yr5 mock‐inoculated—yr5 mock‐inoculated	4. Incomplete isogenicity transcripts