Extended Data Fig. 3: PCA compression of RPPA data and selection of core network components.

(A) PCA compressed RPPA data for TrkA and TrkB cells are plotted in the space of the first two principal components that are normalized by the data variance captured by these components. Following NGF or BDNF stimulation (100 ng/ml) the data points measured by RPPA were clustered in a 115-dimensional molecular dataspace using K-means clustering (K = 2). All data points from NGF-stimulated TrkA cells constitute a single cluster shown in blue, and all data points from BDNF-stimulated TrkB cells form a cluster shown in red. Unstimulated control cells are shown in black. (B) High ranked STV components determine the components of a core signaling network. The changes in individual protein activities or abundances between the centroids of the data point clouds that characterize two different cells states were projected onto the STV to determine protein ranks. Resulting high rank proteins constitute the nodes of a core signaling network.