Abundance in Protein Networks Figure 3. Relationship between protein degree and abundance in the raw yeast Y2H Ito PPI network [7] using the western blot abundance measurements of Ghaemmaghami et al. [42]. (A)–(D), see Figure 1 legend. doi:10.1371/journal.pone.0005815.g003 the number of interactions a protein is involved in is related to its cellular concentration. Such an interpretation would suggest that a salient probabilistic element exists in the interactome. However, regardless of the extent of the probabilistic behavior, it is well established that there exist stable protein complexes [47]. Therefore, it is of interest that we find all of the raw Y2H PPI data sets, whether individual Ito, Uetz, or combined, to have no correlation between degree and abundance (Table 1). All correlations coefficients are very small, lying between 20.07 and 0.04, and all P-values, for Pearson correlation coefficients, are greater than 0.02, although for the individual Ito and Uetz data sets they range from 0.06 to 0.92. When using the GE and WB abundance measurements, correlation coefficients have absolute values of less than 0.05 and P-values are greater than 0.22. P- values are smallest for the FC abundance measurements and the reasons why are not immediately clear. Figures 3A and 3B show the non-averaged and averaged data, respectively, for the Ito PPI network using the WB protein abundance measurements. It is clear from both plots that no relationship exists between degree and abundance. In order to further clarify the differences between PPI networks determined from the Y2H and the affinity purification methods we analyzed abundance distributions by degree for proteins appearing in both the raw Ito PPI and WB abundance measurement data sets. Figures 3C and 3D show the total abundance distribution and the distributions for each degree, respectively. The total abun- dance distribution is essentially normal and notably very similar to that of the TAP Gavin PPI data set (Figure 1C). Additionally, Figure 3D shows that the distributions for each degree are symmetric about their averages and also clearly illustrates the lack of a degree/abundance correlation. Therefore, when compared against the results for the raw TAP and HMS-PCI data sets, we must conclude that the raw Y2H PPI data sets contain no degree/ abundance relationship. Furthermore, we must also affirm that the PLoS ONE | www.plosone.org 6 June 2009 | Volume 4 | Issue 6 | e5815