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Supplementary material Supplementary Table 1 – The cytokinesis cofactor profile. The table shows all genes that are a) induced (log2(fold change) > 0.7) in swi2, snf1 (in minimal media) and bur6 (YPD) b) repressed (log2(fold change) < -0.9) in rsc3 and c) not significantly responding (-1 < log2(fold change) < 1) in rsc30. Only 18 genes satisfy this criterion, eight of which belong to module #126 and three are cell wall associated. Out of the remaining eight genes, six are structural enzymes in glycogen or related metabolism and two are uncharacterized. Supplementary Figure 1 – Joint distribution of the number of genes and properties in modules. The graph shows the fraction of modules with particular numbers of genes and properties. We used logarithmic size bins. Supplementary Figure 2 – Correlation of module #232 (Ribosomal Proteins) and module #524 (RNA processing). The graph shows the mean expression of the two modules across more than 1500 gene expression profiles. Supplementary Figure 3 – Correlation between expression of the HAP4 gene and of the Hap4regulon. The graph shows the expression of the HAP4 gene and the mean expression of module #536 across more than 1500 gene expression profiles. Supplementary Figure 4 – Hog1-Ssk1 dependent repression of module #524. We plot the change in expression of all the genes in module #524 (RNA processing) in the wt strain (X axis) and in the hog1, ssk1 and ste11 strains (Y axis), 20 minutes after treatment in KCl. The strains that disrupt the osmotic stress-specific signaling pathway (ssk1, hog1) exhibit reduced repression in both high (a) and low (b) KCl doses. The ste11 strain behaves similarly to the wildtype. 2 Supplementary table 1 Gene Process DSE1 DSE3 DSE2 AMN1 EGT2 CTS1 BUD9 SCW11 YRO2 WSC4 YGP1 ENO1 TDH1 PGM2 GSY2 GCV1 ADE17 YER067W YOL106W Mod #126 Mod #126 Mod #126 Mod #126 Mod #126 Mod #126 Mod #126 Mod #126 cell wall cell wall cell wall glycolysis glycolysis glycogen glycogen glycogen purines unknown unknown snf1 minimal media 2.44 0.88 1.83 1.42 1.75 1.37 0.85 2.22 3.72 2.53 1.96 0.96 1.69 0.86 1.69 1.26 0.77 1.29 1.63 swi2 minimal media 2.24 0.78 1.60 1.13 1.47 0.99 0.73 1.80 3.86 2.42 2.03 1.11 1.54 0.92 1.19 1.57 0.84 1.31 1.54 3 rsc3 rsc30 bur6 -2.42 -1.88 -2.75 -1.97 -1.18 -1.55 -0.92 -2.74 -2.04 -1.57 -1.30 -1.55 -2.74 -2.16 -1.55 -2.14 -1.35 -1.66 -1.79 -0.22 0.38 0.41 0.01 -0.80 -1.00 0.05 -0.26 -0.74 0.48 -0.32 -0.62 -0.59 -0.61 -0.75 0.76 0.52 -0.61 -0.54 0.79 1.11 1.33 0.99 1.01 1.58 1.24 0.84 1.23 1.58 1.01 0.78 2.13 4.35 2.21 1.70 1.51 2.83 1.43