Here we collected transcriptome and hormone profiles of these combinatorial mutants along a detailed time course and quantified how interactions among the four major sectors JA, ET, PAD4 and SA regulate the dynamic plant transcriptome in response to flg22 treatment. We show that sector interactions, rather than individual functions, dominated the regulation of the transcriptome response, and that buffering was extensive in the network. We further demonstrated several specific cases where the functional mechanisms inferred from shallow network perturbation did not reflect the regulation of the flg22-responsive and JA-ET-PAD4-SA network-dependent transcriptome. Our analysis spotlights a complex biological network that resists a classical genetics approach, a network where single-gene mutant analysis sometimes leads to incomplete or incorrect descriptions of component functions. We demonstrate the effectiveness of a systems biology approach, network reconstitution, to elucidate dynamical component functions of the plant immune signaling network.
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