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Arabidopsis defense response against the bacterial pathogen, Pseudomonas syringae, is a complex and highly regulated process. Previous studies have identified many critical genes encoding regulators that govern innate immunity, but comprehensive transcriptome analysis of corresponding mutants is lacking. Using a custom microarray, we profiled the transcriptome of many mutants with mutations in critical regulatory genes affecting Arabidopsis disease resistance. We show that previously identified mutants affecting the salicylic acid (SA) sector of the defense network have similar transcriptional profiles. Surprisingly, jin1, jar1 and dde2 that are involved in jasmonates (JA) sector did not show major transcriptome changes, while coi1 did. Further analysis revealed that the phytotoxin, coronatine, secreted by P. syringae, is responsible for nearly all COI1-mediated responses.