Within each synonymous group, all pair-wise PCCs were calculated and then summarized to one value indicating the expression correlation of this group. The expression correlations of all synonymous groups at one level were then averaged into an overall value for a dataset (see Method section for details). The correlations of synonymous groups for 30 datasets at three different levels were depicted in parallel in Figure 1A . It is noticeable that the synonymous probesets at Affy-protein level show higher correlations than those at gene level, but the synonymous ones based on our protein level annotation show even higher correlations consistently over 30 datasets (p < 0.05 for 30 datasets under student's t-test, see Additional file 2 for details). The comparison proves the rationality and necessity of our protein-level probeset annotation.