Density plots of the in-degree z-scores. The plots show the density estimates of the in-degree z-scores for [1,10,11]. The zero line is present to distinguish between positive and negative z-scores. The distribution reported by Ito and coworkers  shows a high concentration of data points that have positive z-scores, whereas the data reported by Gavin and coworkers  and Krogan and colleagues  have maximal density for negative z. Systematic artifacts such as auto-activators in the yeast two-hybrid (Y2H) system and protein abundance in affinity purification-mass spectrometry (AP-MS) might play a role in off-zero mean of these density plots. Restricting to the Ito-Core set appears to eliminate the effect from the Ito-Full set.
Chiang et al. Genome Biology 2007 8:R186 doi:10.1186/gb-2007-8-9-r186