Figure 3.

Refining network structure with double-mutant data. (a) Pseudocode of the extension utilizing double-mutant data. Acc_-j(i) indicates the accessibility list of gene i in the absence of gene j. i, j, k, and l are arbitrary indices for genes in the network. (b) An example of a three-gene cycle (top), its single-mutant accessibility lists (bottom left) and a reconstruction based on that data (bottom right). (c) The double-mutant accessibility lists for the cycle in (b) and the reconstruction process. For each set of double-mutant data (left), edges revealed to be indirect are removed from the reconstruction (right). The notation [1] 2 > indicates the accessibility list of gene 2 in a strain in which gene 1 is already perturbed. (d) A network in which genes 1 and 2 redundantly regulate gene 3 (right), and single-mutant and double-mutant accessibility lists for the network (left). (e) A network in which gene 1 regulates the activity of gene 3 indirectly by modifying the activity of a direct regulator, gene 2 (right); single- and double-mutant accessibility lists (left).