Flood minimization of the E. coli gene regulatory network for different scenarios. (A) Stationary phase scenario, where the source node is sigma factor σ38 and reporter nodes are genes that were found to be over expressed in the stationary phase in transcriptional profiling experiments. (B) Exponential growth scenario, where input signals are the sigma factors σ70, σ38 and σ54; reporter nodes are genes with Gene Ontology annotation related to the exponential cell growth. (C) Transition phase scenario, where input signals are the σ70 and σ38 sigma factors; reporter nodes are the top genes expressed during the transition from exponential to the stationary phase. Solid and dash-dot lines depict link and node removal, respectively; p-value is calculated by the hypergeometric distribution with multiple hypothesis testing correction (Bonferroni); “flood threshold” refers to the threshold t in the methods section; “reachable” network refers to the complete sub-network of nodes that is connected, directly or indirectly, to the sigma factors that are active in the corresponding condition (both topology and directionality is used to extract the reachable network); reduction is shown as a percentage of the reachable network.