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. 2013 Jan 31;8(1):e55724. doi: 10.1371/journal.pone.0055724

Figure 2. Ingenuity Pathway Analysis (IPA) prediction and analysis of signal transduction networks for the 288 proteins in the VCP interactome in AGS cells.

Figure 2

(A) AGS cells overexpressing VCP-Flag or mock infected were pretreated 10 µM MG-132 for 3 hr and co-cultured with H. pylori for 6 hr, then immunoprecipitation was performed using anti-Flag antibody affinity gel and the precipitated proteins examined on silver-stained SDS gels (top panel) and immunoblots using anti-Flag antibodies (bottom panel). The lines on the right of the gel indicate where the gel was cut and the sections digested with trypsin and the peptides analyzed by mass spectrometry analysis; the identified VCP-binding proteins are listed in Table S2. (B) Proportionately drawn Venn diagram analysis of the total proteins in Mock and VCP co-immunoprecipitates. (C) The networks were generated by the shortest path algorithm of the Ingenuity Pathway Analysis (IPA) software using the list of 288 proteins in VCP co-immunoprecipitates identified by LC-MS/MS analysis (Table S2). The lines connecting molecules indicate molecular relationships.