Summary of gene circuit performance under various scenarios of data availability.

Scenario names are described in Table 4. Column 1–4: for each scenario, the number of selected/total runs is given; the minimum and median RMS score of the selected runs is indicated. The horizontal bar graphs to the right represent fractions of the selected runs in which specific regulatory mechanisms were found to be present. Smaller bars correspond to single interactions, larger to summaries of multiple interactions. Blue column: alternating cushions refers to the inhibiting interactions of hb and kni, as well as gt and Kr. Green columns: auto-activation is defined as a gene having an activating interaction with itself. Red columns: shifting domains are defined in terms of the following net effects between overlapping gap domains (see main text for the definition of net effects): posterior hb represses posterior gt, gt represses kni, and kni represses Kr (cf. Figure 6C). Orange column: the net repressive interaction between hb and Kr, as calculated for other overlapping gag domains above. Bars indicate net repression of Kr by Hb, which is the standard situation in protein-based circuits, while most mRNA-based circuits show net repression of hb by Kr. Purple column: Bcd and Cad activation is defined as the fraction of gene circuits in which Bcd activates all four gap genes and Cad activates gt and kni. Brown column: Tll and Hkb inhibition is defined as Hkb inhibiting hb, while Tll inhibits the other three gap genes. See text for details. The results summarised here are based on the interconnectivity matrices shown in Text S3.