Validation and refinement of Swi4 transcriptional cascades. Yeast genome microarrays were used to explore three transcriptional cascades from Model 1 involving the transcriptional regulators Swi4p, Sok2p, and either (a) Msn4p, (b) Hap4p, or (c) Yap6p. Bar charts show the expression coherence of genes regulated by Msn4p, Hap4p, or Yap6p in knockout strains swi4Δ, sok2Δ, msn4Δ, hap4Δ, and yap6Δ. Coherence scores more extreme than ± 0.7 are significant (p < 0.01, dotted lines). (d) Results are also shown for genes bound by Msn1p as representative of an unrelated model not targeted by these perturbations. This analysis provides validation for the Msn4 and Hap4 pathways and disambiguates the role of each pathway interaction as activating (Swi4 interactions) or repressing (Sok2 interactions) downstream genes (e). The Yap6 pathway hypothesis is not supported by this analysis.