Integrated Functional Analysis of the Nuclear Proteome of Classically and Alternatively Activated Macrophages

Figure 10

Network analysis of proteome datasets in M2 polarized (vs. M0) Mφ. Integrated nuclear proteome of M2 (vs. M0) Mφ was developed as described in Materials and Methods. Ingenuity Pathway Analysis of the differential proteome datasets presented in S1 Table was performed to develop the networks. Shown are changes in abundance (a), RoR values (b), and phosphorylation (c) of protein spots linked to disease and function networks in M2 vs. M0 Mφ. In the networks, the intensity of pink/red and green colors shows the extent of increase and decrease in protein abundance, RoR values, or phosphorylation levels, respectively, in M1 (vs. M0) Mφ. Brownish orange node/lines and blue node/lines show predicted activation and inhibition, respectively, of a pathway. Gray and yellow lines are used when putative effect is not completely understood. Note that several molecules that are predicted to be associated with increase in transcription/protein and lipid synthesis and cell proliferation and survival were changed in abundance as well as S-nitrosylation and phosphorylation levels in M2 (vs. M0) Mφ.

(a) Abundance

(b) RoR

(c) Phosphorylation