Abundance in Protein Networks Figure 1. Relationship between protein degree and abundance in the raw yeast TAP Gavin PPI network [5] using the western blot abundance measurements of Ghaemmaghami et al. [42]. (A) All data points, i.e., each protein’s degree and abundance is plotted; (B) averaged data where log2(abundance) values were averaged over proteins having the same degree; (C) total normalized abundance distribution, binned in integer values of log2(abundance), for proteins appearing in both PPI and abundance measurement data sets; (D) normalized abundance distributions for each degree where frequencies are shown by color: most yellow signifies smallest nonzero value and most blue represents values larger than 0.25. Best-fit line to data in (A) also shown in (D). doi:10.1371/journal.pone.0005815.g001 Gavin PPI network using the WB abundance measurements [42], and Figure 1B shows the general trend where log2(abundance) values were averaged over proteins having the same degree. The Pearson correlation coefficient for this latter averaged data is 0.52 and the corresponding P-value is less than 0.0001. Similar plots are obtained for the other raw yeast TAP PPI data sets and also when using the FC (protein) and GE (mRNA) abundance measurements. The results for the E. coli TAP data sets are almost identical to those of the yeast TAP sets (Table 2), with Pearson and Spearman correlation coefficients lying between 0.11 and 0.46 and all associated P-values less than 0.0001. Figures 2A and 2B show the non-averaged and averaged data, respectively, for the Butland PPI network using the GE measurements of Covert et al. It is clear that there is a definite propensity, although slight, for proteins of increasing degree to have higher abundances. The observed correlations could be artificial if the abundance distributions of the proteins at each degree are skewed. However, this notion can be discounted as we are finding statistically significant correlations for non-averaged data. Nonetheless, we investigate the abundance distributions by degree to further establish the authenticity of the degree/abundance relationship in the raw TAP PPI networks. For proteins appearing in both the raw Gavin PPI and WB abundance measurement data sets, we show the total abundance distribution (binned in integer values of log2(abundance)) in Figure 1C and for each degree (as a color map) in Figure 1D. The total abundance distribution is seen to be very close to normal and the distributions for each degree are also reasonably symmetric about their averages. Note that Figure 1D reflects the general trend of the averaged data in Figure 1B. These observations are echoed for the E. coli TAP Butland PPI network PLoS ONE | www.plosone.org 4 June 2009 | Volume 4 | Issue 6 | e5815