Figure 1.

Wiring diagrams for example network models. (a) Model 0, showing regulatory pathways that have unique functional annotations. (b,c) Model 1, showing regulatory pathways downstream of SWI4 and SOK2 with ambiguous functional annotations (several would be consistent with the observed expression responses: two possibilities are shown in (b) and (c), respectively). In the models, a connection from gene a to b represents the experimental observation that the proteins encoded by a and b physically interact in a protein-protein interaction (dotted links), or that the protein encoded by a binds the promoter of b (solid links). Each gene is either defined by an original knockout (red nodes), a differentially expressed effect (yellow nodes), or a signal transducer that was chosen for follow-up perturbation (gray nodes). Functional annotations (edge colors) are uniquely determined in (a) whereas multiple annotations are possible in (b) and (c) based on the available data. Diagram layout is performed automatically using the Cytoscape package [21].