Fig. 2

Canonical pathways form groups for each individual protein. The table on the left contains the name of each pathway in the cluster, as well as the proteins for which the pathway enriches. To illustrate the interrelationships of the proteins in each cluster with upstream regulators determined by IPA, the proteins that enriched for the pathways in clusters 1, 2, and 3 as well as upstream regulators were visualized as a network using IPA. Downstream proteins that were detected in the proteomics experiment are denoted by fold change and p values beneath them. Red color indicates an upregulation and green a downregulation with color intensity related to expression value. Upstream regulators are listed in the table to the right of the figure and contain the downstream proteins effected. Upstream regulator are colored with orange (upregulation) or blue (downregulation). The lines connecting various proteins are meant to describe the predicted effect that the observed change has on that particular relationship. A blue line would suggest that due to the differential expression of the upstream protein, it is having an inhibitory effect on the downstream target. With this graphic representation of the networks, the complex interactions and nodes of intersection can be presented. For example, note that RICTOR, one of the top upstream regulators identified, is central to both clusters 1 and 2