*3.6. Integration with Other ZIKV PINs*

Our work builds on three previous physical interaction networks of host and ZIKV proteins [19–21]. We integrated our PIN with the published networks to evaluate the level of overlap between the four PINs (Figure 4A; Table S11). No common hit was shared by all four PINs and pair-wise overlaps ranged from 1 to 50 hits, suggesting that the ZIKV–host protein interacting network is still far from reaching saturation (Figure 4A,B).

We identified five highly internally connected clusters among the integrated PIN (Figure 4C). All five clusters contained components of the ZIKV PIN from this study. Four of them were enriched in proteins involved in the following: (a) anaphase promoting complex (APC)-dependent proteasomal ubiquitin-dependent protein catabolic process (GO31145); (b) protein amino acid N-linked glycosylation via asparagine (GO18279); (c) protein folding (GO6457); (d) regulation of transcription (GO45449); and (e) histone H2B ubiquitination (GO33523).

Finally, 14 unique nodes of our merged ZIKV PIN (9.3% of the data set) have been shown to be important for proper replication of different Flavivirus (Table S12) [38–40], suggesting that our network also contains proteins that could explain the mechanisms of ZIKV replication and help identify therapeutic targets.

**Figure 4.** Integration of ZIKV PINs. (**A**) Network of the interactions identified by this study, Scaturro et al. 2018, Shah et al. 2018, and Coyaud et al. 2018. The color legend is depicted on the upper left-hand corner. (**B**) Graphic representation of common preys according to the bait and study in which they were identified. (**C**) Clustering of bait sets according to overlapping protein complexes among the integrated network using ClusterONE (Version 1.0) [29]. Gene ontologies of these networks were obtained by the Cytoscape plugin, BINGO [30]. GO accession numbers represent the following biological process: GO31145—anaphase promoting complex (APC)-dependent proteasomal ubiquitin-dependent protein catabolic process, GO18279—protein amino acid N-linked glycosylation via asparagine, GO6457—protein folding, GO45449—regulation of transcription, and GO33523—histone H2B ubiquitination. Proteins identified in this study are represented as orange nodes.
