Figure 3. Interaction Profiles of Chromatin Modification-binding Proteins.

Agglomerative hierarchical clustering was performed on the SILAC enrichment values of proteins regulated by DNA and histone methylation to identify proteins with related binding profiles. This analysis includes proteins based on an enrichment/exclusion of at least 1.5 fold in both directions in one of the nucleosome pulldown experiments and excludes factors that were found solely in the DNA pulldowns. Log₂(ratio_for/ratio_rev) is the log2 ratio between the SILAC values (ratio H/L) of the forward and reverse experiments. Enrichment by modifications is indicated in red, exclusion is indicated in blue. Grey bars indicate if proteins were not detected (n.d.) in particular experiments. These incidences were not included in the cluster analysis. Clusters of several known protein complexes and their respective subunits are indicated on the right. For values see Table S2.