Fig. 1

Quantitative proteomic analysis of IFNβ stimulation. a Schematic overview of the shotgun proteomics workflow for analysis of IFN-induced proteome changes. b, c Volcano plot showing differential protein abundance in cells stimulated with IFNβ for 4 h (b) or 24 h (c). Vertical lines denote absolute fold change ≥ 2. Horizontal lines show 5% FDR threshold. d, e Gene Ontology (GO) terms for biological processes (d) and molecular functions (e) significantly enriched among differentially expressed proteins after 4 h or 24 h of IFNβ stimulation. f, g Number of protein-protein interactions in the InBioMap database [19] between differentially expressed proteins after 24 h (f) of IFNβ stimulation, or between cells stimulated for 4 and 24 h (f), arrows, and in 100 randomly rewired networks derived from the same database, histograms. h Enrichment for protein-protein interactions between 3263 curated gene signatures from the MSigDB chemical and genetic perturbations collection, histogram, and the sets of proteins differentially expressed after 24 h of IFN stimulation relative to unstimulated cells or cells stimulated with IFN for 4 h, dotted lines