Mining for meaning: visualization approaches to deciphering Arabidopsis stress responses in roots and shoots

Massive amounts of transcriptomic data documenting plant responses to changes in environment continue to accumulate in online databases. Unfortunately, many of these data sets have not been analyzed in full detail, especially those that involve time course experiments. To gain more knowledge of the successive gene expression events that occur when stress is initiated in one organ and then relayed to another, we have chosen stress response data for Arabidopsis shoots and roots from the detailed time course study of Killian et al. as a promising source to mine. Using refined statistical analysis, modified vector analysis, and a GO enrichment algorithm, more information was revealed concerning the effects of salt and UVB on gene expression events in shoots and roots over a 24-h time period. GeneMania, with in-house modifications, was used to further analyze abscisic acid (ABA) and jasmonic acid-related (JA) gene expression events in salt-stressed roots and shoots. JA effects appeared to be quite distinct in roots when compared to shoots, especially with respect to the expression of members of the negative regulatory JAZ gene family. In contrast, ABA-related gene expression events were more similar in the two organs. Instances of crosstalk between hormones were observed, as were early responses of regulatory genes involved in both auxin and cytokinin signaling. In the case of each hormone class examined, hormone biosynthesis genes were coexpressed with the genes encoding negative regulators of the corresponding signaling pathway. Hypotheses to explain this finding and future experiments to further explore these nonlinear phenomena are proposed.