Given protein-protein interaction data from HPRD or IntAct, we first transformed the binary relations of protein accessions to IPI-IPI pairs, and also got the corresponding Gene-Gene pairs. For each PPI, we assembled the PPI probeset pairs and the GGI probeset pairs as illustrated in Figure 3 , where PPI pairs are those associated with the interacting IPI IDs while GGI pairs are those associated with the corresponding Gene IDs. For all probeset pairs associated with the IPI-IPI pair (PPI pairs) and those associated with the corresponding gene-gene pair (GGI pairs), the PCCs were calculated and averaged into a PPI PCC and GGI PCC, respectively. These PCCs of interacting pairs were further calculated to obtain the accompanying false discovery rates using the SPLOSH FDR estimation method.