Changes in gene expression form a key component of the molecular mechanisms by which plants adapt and respond to environmental stresses. There is compelling evidence for the role of stimulus-specific Ca(2+) signatures in plant stress responses. However, our understanding of how they orchestrate the differential expression of stress-induced genes remains fragmentary. We have undertaken a global study of changes in the Arabidopsis transcriptome induced by the pollutant ozone in order to establish a robust transcriptional response against which to test the ability of Ca(2+) signatures to encode stimulus-specific transcriptional information. We show that the expression of a set of co-regulated ozone-induced genes is Ca(2+) -dependent and that abolition of the ozone-induced Ca(2+) signature inhibits the induction of these genes by ozone. No induction of this set of ozone-regulated genes was observed in response to H(2) O(2) , one of the reactive oxygen species (ROS) generated by ozone, or cold stress, which also generates ROS, both of which stimulate changes in [Ca(2+) ](cyt) . These data establish unequivocally that the Ca(2+) -dependent changes in gene expression observed in response to ozone are not simply a consequence of an ROS-induced increase in [Ca(2+) ](cyt) per se. The magnitude and temporal dynamics of the ozone, H(2) O(2) , and cold Ca(2+) signatures all differ markedly. This finding is consistent with the hypothesis that stimulus-specific transcriptional information can be encoded in the spatiotemporal dynamics of complex Ca(2+) signals in plants.