Figure 2

A and B, number of gene pairs detected by the TC method in comparison to those of the LC method and the PCC method inferred from the yeast cell cycle dataset of Cho et al. [18] at two different p-value thresholds. The numbers in parentheses are the whole number of gene pairs detected by the corresponding method. The percentage of the additional number of gene pairs inferred only by the TC method in the text is calculated in a way exemplified in the following by a comparison with those resulted merely from the PCC method at the p-value threshold of $2.7{\text{e}}^{-3}:\frac{60044+5251}{4955+126619}=49.6\%$. C and D, number of process-identity pairs among the detected pairs from the three methods; E and F, number of known protein interactions (including protein complexes) in collection dataset of protein interactions [21] among the inferred gene pairs from the three methods.