Bootstrap analyses of the network. (A) The transcriptional network with edges colored from red to green, and increased thickness, with increasing bootstrap confidence. (B) Correlation between observed and predicted gene expression averaged over experimental conditions not used to infer the bootstrap networks (i.e. the hold-out set). Correlations are shown for individual genes, modules (average correlation for each gene in the module) and a theoretically optimal prediction (predicted expression equal to the average expression profile of the genes in the module). (C) Fraction of genes and modules with a significant correlation between observed and predicted gene expression in each experiment when that experiment was removed before inferring the network.