Figure 4. Protein complexes and protein-protein interactions.
(A) Schematic illustration of interactions that appear between and within complexes. In (B) E. coli and (C) S. cerevisiae we determined the number of binary-Y2H and co-complex interactions between proteins in the same complex as well as within complexes. As a random null model we resampled proteins in complexes 10,000 times. Our results in the upper panels indicate that interactions between complexes appear diluted in all interaction sets (P < 10−4) while interactions in the same complexes seem to be enriched (P < 10−4). Analogously, we investigated interactions between essential proteins in both organisms (lower panels), confirming an enrichment of PPIs within complexes compared to between-complexes in both organisms (P < 10−4). In (D) we calculated the fraction of essential genes in each complex. As a null-model, we randomly sampled essential genes 10,000 times, indicating that complexes generally do not randomly contain essential proteins. Notably, complexes with a very low/high fraction appear to show a significant enrichment of essential genes.