FIG. 1.

Cluster analysis of proteomic data identifies YPL047W as a candidate subunit of SAGA. The cluster diagram on the left shows the unsupervised hierarchical clustering of proteomic data from replicate immunoaffinity purifications of each component of TFIID and control purifications (41). The enlargement on the right expands the cluster display where a pattern of proteins copurifying with a distinct set of TAFs is observed. This cluster of proteins includes all of the previously characterized components of SAGA and a protein corresponding to the uncharacterized ORF (uORF) YPL047W. The SAGA proteins are clustering together with the five TAFs known to be shared by TFIID and SAGA. These shared TAFs are labeled with an asterisk. The estimated relative abundance of each identified protein, PAF (see Materials and Methods), is designated by a shade of red. PAFs of proteins identified in control experiments are indicated by shades of green. A square is black if the protein was not detected from the computational analysis of the experiment's mass spectrometry data. The cluster diagram on the left suggest additional groups of protein associated with specific TFIID subunits that are not addressed in this report (McAfee et al., unpublished).