Design and optimization of the computational model. Design and optimization of the computational model. (A) Illustration of the transcriptional interactions in the model mapped on typical functional domains/cell types of SAMs. (B) The 229 parameter sets from the optimization procedure, displayed using principal component analysis (first and second principal components: e1, e2). The color scale represents the variation of equilibrium KAN1 expression between the wild type and a perturbation (transient ubiquitous CLV3 expression). The gray disk is centered at the parameter set used in all spatial example simulations (Supplementary Table 8). In (C–F), first column shows Confocal side views of SAMs showing cell boundaries (red) and RNA or protein distribution domains (green). Corresponding gene names are given on each panel. Scale bar shown in (C) represents 25 μm (same for C–F). Second column: Templates used for optimization showing corresponding gene expression patterns (green). Third column: Simulation output from the example optimized parameter set. The color scale label ‘normal’ indicates the template defined gene expression level. (C–E) Expression patterns, templates and optimized model for WUS (taken from Yadav et al, 2009), CLV3 (taken from Reddy and Meyerowitz, 2005) and KAN1, respectively. (F) Distribution of WUS protein in the SAM (taken from Yadav et al, 2011) and in the model. The color scale for WUS concentration in the model is capped at the concentration value of WUS repressing KAN1 to half its maximal expression (kw/K). Ram Kishor Yadav et al. Mol Syst Biol 2013;9:654 © as stated in the article, figure or figure legend