Categorizing Biases in High-Confidence High-Throughput Protein-Protein Interaction

We characterized and evaluated the functional attributes of three yeast high-confidence protein-protein interaction data sets derived from affinity purification/mass spec-trometry, protein-fragment complementation assay, and yeast two-hybrid experiments. The interacting proteins retrieved from these data sets formed distinct, partially overlapping sets with different protein-protein interaction characteristics. These differences were primarily a func-tion of the deployed experimental technologies used to recover these interactions. This affected the total cover-age of interactions and was especially evident in the re-covery of interactions among different functional classes of proteins. We found that the interaction data obtained by the yeast two-hybrid method was the least biased toward any particular functional characterization. In contrast, in