Figure 3

Three gap filling steps suffice to fully connect inputs with their respective outputs. The figure displays the difference between the initial (NR1) and final (NR2) networks. (a) Connection of the glucose subgraph to the main pathway. This connection required one abstract state, which is active in the presence of glucose as long as none of the stresses are active, and which activates sumoylation and inhibits phosphorylation of Snf1. It also activates the phosphorylation of Msn2. (b) Adaptation of transport reactions. The nuclear localisation pattern could only be reproduced if both import and export are regulated, otherwise the localisation oscillates. In addition, we added a direct edge from salt stress to inhibit Snf1 nuclear localisation, to account for the observation that Snf1 is phosphorylated but not nuclear on salt stress. (c) Deubiquitylation of Rod1. An unknown deubiqitylating enzyme was added, acting on Rod1. Faded nodes and edges were part of the initial network reconstruction (NR1), while nodes and edges with full colours were added to NR2 during the network refinement. The gap filled NR2 Cytoscape file is attached as Supplementary file 6.