For all datasets, we observed strengthened expression correlations between interacting proteins under the PPI schema relative to the GGI schema. Taking the GDS987 dataset including 41 arrays as an example ( Figure 4A 153, respectively, and the former was significantly smaller than the latter (Kolmogorov-Smirnov test p value is 9.9E-12). Summarizing the comparisons at the positive side and the negative side, we conclude that the expression correlation between interacting proteins is strengthened when the non-interacting protein pairs are excluded from the interacting gene pairs, that is, with the PPI PCC calculation in place of the conventional GGI PCC calculation.