Fig. 3. Structure-function analysis of chromatin regulatory complexes.
For each complex (AH), all genes with significant changes (p<0.05, FC>1.7) in any single mutant are shown, yellow indicating up-, blue indicating downregulation and black indicating no change, relative to the average wt and scaled as in Fig. 1. If a gene is not depicted, then no change in expression is observed outside the thresholds p<0.05, FC>1.7. Fig. S2 depicts all 32 complexes. (A) HDAC (B) SAS (C) HIR (D) Sir (E) SWR1, without Bdf1 as different isolates of bdf1Δ gave different results. The apparent lack of “downregulation” of the deleted gene in swc7Δ and swc3Δ (right hand box) is due to very low expression levels. All such mutants were PCR-verified for carrying the deletion (Supplemental Experimental Procedures). (F) Isw1a and Isw1b (G) Rpd3S and Rpd3L. Ume6 is not shown due to aneuploidy. (H) SAGA. The dendrogram was generated by hierarchical clustering. The grey line indicates that no probe for SUS1 is present on the array. (I) A network of SAGA subunit relationships generated using an edge-weighted, spring-embedded network algorithm (Shannon et al., 2003), revealing connections between submodules.