Figure 2

The regulatory structure of the Snf1 pathway. The regulatory graph depicts the information flow through the NR1 network as a bipartite-directed graph. Elemental reactions (red nodes) produce or consume elemental states (blue nodes) via reaction edges, which correspond to the edges in the reaction graph (Figure 1). The elemental states in turn influence the elemental reactions via contingency edges, and they define contextual constraints on reactions. The inputs in form of external stimuli can be found at the top of the picture, as grey nodes with node names in square brackets. The cytoplasmic reactions and SNF1 complex formation are found in the middle part, and the nuclear reactions at the bottom with the transcriptional output again as grey nodes with names in square brackets. Information passes through the network along the unidirectional edges, either by production (blue edges) or consumption (purple edges) of elemental states by reactions, or by the regulatory effect of elemental states on elemental reactions. Positive contingencies from activating states to activated reactions are denoted in green, while inhibitory contingencies appear in red. More complex requirements, such as formation of the active forms of the SNF1 complex, are defined by Boolean states that are indicated as white triangles (AND) or diamonds (OR). The compartment borders in grey represent the plasma membrane and the nuclear membrane, and have been included as visual guides but carry no information. At the center, we have the three active forms of the SNF1 complex; SNF1*CYT, SNF1*VAC and SNF1*NUC, that are localised to the cytoplasm, the vacuole and the nucleus, respectively. Information can only pass along the direction of the edges, and we can follow them from inputs to outputs. In this network we have four inputs: The three grey stress inputs to the upper right, and extracellular glucose to the upper left. The last is part of an unconnected subgraph, highlighting the fact that we do not know how the glucose signal is sensed by the pathway. The original NR1 Cytoscape file is attached as Supplementary file 5.