Figure 4. The relationship between the numbers of predicted PPIs with protein family sizes and protein lengths on YD and MD sets.

The numbers of PPI candidates are highly correlated with (A) the number of homologous proteins (family size) and (B) protein sequence lengths of known PPI templates using generalized interologs mapping method (black lines) with joint sequence similarity (e.g., E-value ≤ 1 × 10⁻⁴⁰). Conversely, the numbers of predicted PPIs of our method (red lines) are lightly influenced by the protein family sizes and lengths. (C) For a known PPI, the number of homologous proteins in mouse is significantly greater than the one of yeast. For example, the number of homologous proteins of a zinc-finger (PF00096) protein in mouse and yeast are 275 and 24, respectively.