Perturbation Biology: Inferring Signaling Networks in Cellular Systems
Figure 7
The distribution of edges in all network models and average network model.
The probability distribution of edge values (wij) after BP (A, left) are similar to the histograms of the corresponding interactions after decimation (A, right). An interaction strength is nonzero when it has high amplitude and frequency in solution space. We generate instantiated models with BP guided decimation algorithm followed by gradient descent optimization. According to the agreement between the distributions in two panels, BP probability distribution and final model histogram are similar to each other with important exceptions. The BP guided decimation algorithm goes beyond simply sampling from the BP models and may encounter features such as mutual exclusivity during the creation of the final models. (B) The average network model over the 100 best solutions with lowest error capture known interactions such as those in the RAF/MEK/MAPK and PI3K/AKT pathways. The opacities of the edges scale with the absolute probability of the edges. Note that the letter ′a′ is prefixed to so-called activity nodes as explained in Methods section.