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

Figure 9

Network analysis of proteome datasets in M1 polarized (vs. M0) Mφ. Integrated nuclear proteome of polarized and control Mφ was developed as described in Materials and Methods, and protein spots that were differentially abundant or posttranslationally modified in M1 Mφ (fold change: , value ≤ 0.05) were identified by mass spectrometry. Ingenuity Pathway Analysis of the differential proteome datasets presented in S1 Table was performed to develop the networks. Shown are changes in abundance (a, c), RoR values indicating S-nitrosylation (b), and phosphorylation (d) of protein spots linked to disease and function networks in M1 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 change in cytoskeletal organization and cell movement were changed in abundance as well as S-nitrosylation, and molecules predicted to be associated with endocytosis/phagocytosis and cell death/cell survival were significantly changed in abundance and phosphorylation.

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