Fig. 3.

Integrated perspective of a large-scale network perturbation on amino acid biosynthesis. The central GCN4 node anchors a biomolecular gene/protein network expanded to include reactions and metabolites. The network contains condition-specific transcription factor binding, protein–protein binding, enzyme-reaction, reaction-metabolite, and metabolite-protein feedback edges (see node type and edge key). High metabolite interaction density is evident in A, B, and E. The dotted yellow edges emanating from the GCN4 node indicate an interaction found only in the wild type condition (i.e., not in gcn4Δ) Measurement ratios of wild type relative to gcn4Δ were visualized with a log₂ colorbar (see node color key), and gray coloring indicates the lack of a measurement for that node. Findings for individual pathways are discussed in the text.