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. 2008 Mar 14;4(3):e1000029. doi: 10.1371/journal.pgen.1000029

Figure 1. Modeling the Relationship A Is an Upstream Repressor of B.

Figure 1

B in Turn Enhances a Target Gene X. In this example, deleting A will change the state of the target gene from off to on. Therefore, we include A's effect in the corresponding regression model. Deleting B leaves the target gene in the same state as the wild type and its effect is not included. The AB double mutant is also not expected to deviate from the wild type despite the significance of the A deletion. Since A's effect is already included in the model for this contrast, it must be offset by the interaction term. We conclude that if A is enhanced by the signal, A represses B, and B enhances X, the corresponding best-fit regression model will include coefficients for A and an interaction term. Similar logic applies to the case in which the signal represses A. The signal represses A, thus deleting A has no downstream effects. We expect only the coefficient corresponding to the downstream gene in the best-fit model.