Extended Data Fig. 5: Hypothesis-driven and systematic data integration.

(a, b) Intensity of the indicated host protein measured by mass spectrometry in SK-N-BE2 cells, expressing the given VZV ORF or from the background(Methods). Median and 95% confidence intervals are indicated (n = 4 independent experiments per ORF; two-sided Wilcoxon rank-sum test; Benjamini-Hochberg adjusted). (c) Western blot analysis of IFI16 in HEK293T cells after co-transfection with HA-GFP, -ORF61 or -ICP0. Mean +/− SEM are indicated (n = 3 independent experiments; paired one-way ANOVA test, Bonferroni adjusted). A representative blot is presented in Fig. 4b. (d) Immunofluorescence analysis of HFF cells mock- or recombinant HA-ORF61 VZV-infected for 8 h, treated or not with the proteasome inhibitor MG132. HFF cells were stained for IFI16, VZV and with DAPI, and analysed at 20x magnification. Representative of n = 3 independent infection experiments. Analysis of nuclear intensities is summarized in Fig. 4c. Scale bar = 50 µm (e) Validation of the knockdown of UBXN7 in HFF cells by immunofluorescence analysis. Scale bar = 100 µm (f) Network diffusion analysis of VZV ORFs. Interactome and effectome data were mapped onto the cellular gene network ReactomeFI. Effects were used to weight the random diffusion, resulting in several subnetworks of given minimal edge weight and average effect-target path length. Comparison between the ‘real data’ and randomly permuted networks of given minimal edge weight defines the optimal subnetwork with the best proximity between targets and effects. The displayed subnetwork connects targeted, affected and intermediate proteins and provides p-value which evaluate the significance of the connections as compared to the random network. (g, h) Altered subnetworks of ORF12 (g) and ORF9 (h) resulting from the network diffusion analysis. Connections featured in Fig. 4g and h are indicated in blue. Gene names and nature of the connections (for example protein-protein complex; activation; expression control) can be browsed on interactive versions in Supplementary Data.