(A) Consolidates various key statistics shown in Figures 1and 2 for the ribosome and proteasome as well as for a large number of protein complexes. We list all protein complexes from the MIPS catalog having at least 10 open reading frames (ORFs). The complexes are divided into three classes: permanent, transient, or other (see below). Some complexes can be divided into smaller subcomplexes (e.g., the ribosomes) as indicated. The table lists (from left to right) the average expression level of the complex, the median normalized difference (see Fig. 1A), the average correlation for the cell cycle and Rosetta experiments (see Fig. 2), the negative logarithm of the P-value of the average correlations in both experiments (see Fig. 2), and the size of the complex in terms of the number of ORFs.
In general, the P-values for the average correlations are very low for most of the permanent protein complexes [accordingly, −log10(P) is very high], indicating that these averages are significantly greater than for random groups of proteins of the same size. The same cannot be observed for the transient protein complexes, for which the correlation averages are usually much smaller.
The section “other” at the bottom ofA contains complexes that are either difficult to classify as permanent/transient or for which, as a result of very small turnover rates, down-regulations of mRNA levels take a very long time to affect protein abundance. The H+-transporting ATPase can be thought of as containing a mixture of permanent and transient components at the same time (P. Kane, pers. comm.). The nuclear pore complex (NPC) and the TRAPP complex are known to have low turnover rates (Bucci and Wente 1997; Winey et al. 1997; Sacher et al. 1998; Barrowman et al. 2000). The NPC has relatively small average correlations, but this still yields P-values of 10–3 (cell cycle) and <10−4 (Rosetta) because the nuclear pore complex is a relatively large aggregation of proteins, and even these weak average correlations are very unlikely to occur for random groups of proteins of this size. The TRAPP protein complex, while existing throughout the cell cycle, has a low turnover rate and as such its mRNA expression data would not be sufficient for our analysis.
The RNA polymerase holoenzyme is composed of both permanent and transient components. Note that the MIPS complexes catalog does not include the SWI/SNF chromatin-remodeling complex and a subset of basal transcription factors (Wilson et al. 1996) as part of the holoenzyme, thus we list them separately here.
The list does not include those categories from the MIPS complexes catalog that do not really represent protein complexes per se, but rather aggregations of disparate proteins that are involved in similar types of complex interactions, such as the “actin-associated” and “tubulin-associated” protein groups.
(B) Shows a graphical representation of part of the protein complex statistics from A. The abscissa and ordinate represent the average correlations in the cell cycle and the Rosetta data, while the bubble sizes are a function of the normalized differences (larger bubbles represent larger normalized differences). In general, the permanent complexes tend to be located in the upper right region of the plot, whereas transient complexes are closer to the random control in the lower left.
