Figure 2

Orthologous co-expression can be used to predict PPIs. (a) Schematic representation of the method. (b) Interacting proteins are more likely to have an orthologous pair in other species. The percentage of yeast protein-pairs with an orthologous pair from five species (C. elegans, E. coli, A. thaliana, D. melanogaster, and H. sapiens) is shown for the reference and random sets. This property is seen for the four eukaryotes, but not for E. coli. (c) Orthologous pairs of interacting proteins are more likely to be co-expressed than orthologous pairs of random protein-pairs. The percentage of orthologous pairs having significant (P-value < 0.05) correlation of expression out of the total orthologous pairs with available expression data (conserved+expression), and out of the entire reference set (all interactions) is shown for all organisms (including S. cerevisiae). (d) Orthologous co-expression from five species was added and used to predict S. cerevisiae PPIs (red). The resulting predictive power is shown along with the predictive power of S. cerevisiae co-expression (dashed blue), as shown in Figure 1b. Orthologous co-expression was also added to S. cerevisiae co-expression, resulting in an improved predictive power (green).