Fig. 2

D29E induces PTI-associated gene expression that is suppressed by AvrPto. a Expression data for ETI- and PTI-specific marker genes described previously [6]. Gene expression values are RPKM averages of the four independent trials, and the error is one standard deviation based on those four replicate experiments. An asterisk indicates that the gene expression level is significantly different from a mock inoculation (p < 0.05) based on p-values corrected for multiple testing using the false discovery rate. b Venn diagram showing the number of genes whose transcript abundance is significantly increased in response to flgII-28 or D29E expressing CTD⁻/CD⁻, or both [4]. The criteria used are a positive-fold change of 2 or greater, an average RPKM of 3 or greater in at least one treatment, and a p-value of 0.05 or less. These criteria are the same used previously [4]. c Venn diagram including genes either meeting the criteria for a FIRE gene as described previously, or induced by D29E expressing CTD⁻/CD⁻ and then relatively repressed by D29E expressing AvrPto using the same statistical criteria as for the FIRE genes [4]