The illustration of the overall strategy. There are three parts of the strategy for linking signal transduction with gene responses. First, a reverse engineering model is used to reconstruct the regulators' activity profiles and relative regulatory strength from temporal gene expression data. Then the forward simulation model that describes the signal transduction pathway is constructed for simulating the regulatory profiles of the transcription factors. Finally, the forward-simulated transcription factor profiles are used to match with the activity patterns of the transcription factors that were obtained from the reverse engineering.