Figure 5

Overview of the algorithm employed to search in the yeast genome for the abundance of the special topologies necessary for network-dosage compensation. The algorithm takes as input a set of precompiled possible network elements (genes that potentially have a role in transcription regulation within each network), transcription factor binding data for the promoter region of each element, and physical and genetic interaction data among the elements and the transcription factors. The algorithm first searches for all possible two-component networks in which both elements are under the control of the same TF, and could influence their own expression by interacting with that TF directly or indirectly. Then, using the genetic interaction data, it attempts to determine whether the two components are of different regulatory signs and then reach a definitive conclusion on the presence of a dosage compensation motif for each TF-network combination based on the topology of the physical interaction and the regulatory sign. In post-processing, combinations for which a definitive conclusion can be made are manually combined into larger networks and the dosage compensated structures in each are counted.