Plants perceive information from the surroundings and elicit appropriate molecular responses. How plants dynamically respond to combinations of external inputs is yet to be re-vealed, despite the detailed current knowledge of intracel-lular signaling pathways. We measured dynamics of Response-to-Dehydration 29A (RD29A) expression induced by single or combined NaCl and ABA treatments in Arabidopsis thaliana. RD29A expression in response to a combination of NaCl and ABA leads to unique dynamic be-havior that cannot be explained by the sum of responses to individual NaCl and ABA. To explore the potential mechan-isms responsible for the observed synergistic response, we developed a mathematical model of the DREB2 and AREB pathways based on existing knowledge, where NaCl and ABA act as the cognate inputs, respectively, and examined various system structures with cross-input modulation, where non-cognate input affects expression of the genes involved in adjacent signaling pathways. The results from the analysis of system structures, combined with the insights from microarray expression profiles and model-guided experi-ments, predicted that synergistic activation of RD29A originates from enhancement of DREB2 activity by ABA. Our analysis of RD29A expression profiles demonstrates that a simple mathematical model can be used to extract information from temporal dynamics induced by combina-torial stimuli and produce experimentally testable hypotheses.