Figure 4

Molecular pathways of regulated proteins. Proteins and their levels of regulation were imported into the Ingenuity Pathways Analysis (IPA™) tool and interacting pathways were constructed. A, Ontological classifications of all measured proteins (Total) as well as those significantly up- and down-regulated. B, Merged networks, determined by uploading the regulated proteins only into STRING [54, 55] (left), or by uploading all molecules and their degree of regulation into IPA™ (middle). C-F, The top 4 IPA networks, identified at 95% confidence and each of which contained 12 or more “focus” molecules (molecules significantly up- or down-regulated), with pathway names indicated. Solid lines: direct known interactions; dashed lines: suspected or indirect interactions. Significantly regulated proteins identified in either the cytosolic or nuclear fractions were overlaid onto each network; red: significantly up-regulated proteins; pink: moderately up-regulated proteins; grey: proteins identified but not significantly regulated; light green: moderately down-regulated proteins; dark green: significantly down-regulated proteins; white: proteins known to be in network, but not identified in our study.