Figure 3
From: Making the most of high-throughput protein-interaction data
Scatterplot of nin and nout for the AP-MS data of Krogan et al. [11]. Each point in the plot corresponds to one protein. n in is the number of times that the protein was found as a prey; nout the number of prey it found when used as a bait. The two lines mark contours of probability p = 10-4 according to the Binomial model in Equation (3). Outlying proteins (dark blue) show a significantly large difference between nin and nout, suggesting that at least one of them is wrong. For example, if nout >> nin, one possible reason is that a protein is not expressed when used as prey or of such low abundance that it is outcompeted, but when tagged and expressed as a bait, it will identify and pull down its interaction partners as prey. Further validation experiments are needed to determine in each case whether the unreciprocated interactions correspond to false-positive or false-negative observations.