Since the estimated coefficient, 0.5612, is far less than 1, we may conclude that the absolute PCC values of PPI pairs are often larger than those of the corresponding GGI pairs. So the PPI PCC calculation preserves the original positive or negative correlation tendency revealed by the conventional GGI PCC calculation, and strengthens it with larger absolute correlation values. Such correlation tendencies between interacting proteins, especially those negative ones, would very likely be submerged under the Figure 3 Illustration of Entities and terminologies involved in protein-protein interaction. A) Relationship among genes, transcripts, proteins and probesets. B) Two types of pairs mentioned in the text. PPI pair indicates the probeset pair correlating to a real interacting protein pair; while GGI pairs are those probeset pairs correlating to all possible cross-gene pairs. PPI may not exist in all cross-gene pairs.