Figure 1

Schematic diagrams of modules employed. The input S is a spatial signal. (A) In the coherent feedforward module S positively regulates (arrows denoted by filled arrowheads) X and Y which in turn positively modulate the response R. (B) Similar to (A) except X inhibits the response element, representing one kind of incoherent feedforward circuit (see text). (C,D) In the positive (negative) feedback module S leads to the activation of the response R which subsequently activates (inhibits) X via the intermediate feedback element Y . (E) A sample cyclic reaction network is shown. S catalyzes (denoted by a sharp line arrowhead) the conversion of X₁to X₂. (F) The monostable switch module consists of two enzymes S and U acting close to saturation and mediating the production and degradation of X. (G) The bistable switch module consists of a double negative feedback loop. S regulates the production of X and X and Y inhibit one another. (H) In the transcritical bifurcation module X is inhibited by the signal and activates its own production via the feedback element Y . The oscillator module is realized from the topology in (D) with different non-linear interactions (see text). (I) A simple cross section of the cell is shown exhibiting a cell membrane (CM), cytoplasm (C), an organelle (O) and a nucleus (N). The small circles in the cell represent signalling molecules. Gradually graded as well as localized concentration profiles of different signalling entities naturally arise and are transduced through various complex networks which also include global coupling through diffusion.