Figure 1

Data processing workflow. The primary dataset is a complete list of proteins identified in IP experiments that were used to map the Chromatin Central proteomic environment in any of the two yeasts. After removal of ribosomal proteins, all hits together with their A-indices were compiled into a non-redundant master table and grouped according to IP rounds. To accurately determine the scaffold protein complexes, we further removed from the master table proteins having A-index = 1 that were identified only in one IP experiment and common background proteins. Using the average A-index of background proteins as a selection threshold, the remaining proteins were sorted into two large groups: proteins enriched in corresponding IP experiments and proteins whose abundance remained at the background level. Proteins in the first group were considered as genuine interactors and were assigned to complexes, assuming IP experiments in which they were identified. From the second group, only proteins that were validated by a reciprocal IP experiment were assigned to the corresponding complexes.