The properties of hub proteins in a yeast-aggregated cell cycle network and its phase sub-networks

Currently, most researches on the properties of interacting proteins, hubs in particular, are mainly based on an aggregated network of binary interactions. Here, by projecting a yeast-aggregated cell cycle network into four phase (G1, S, G2 and M) sub-networks, we explored the properties of the hubs of the aggregated network. We found, as expected that only 69% (103 of 149) of hubs still act as hubs in at least one of the four sub-networks. Interestingly, those (19%) that are not hubs in any phase tend to perform multiple functions and differ from the others in their network positions. We also analyzed the potential biological features among the dynamic and static hubs. Finally, we investigated the dynamic properties of two complexes, the anaphase-promoting complex and the chromatin-remodeling complex. The dynamic function of the anaphase-promoting complex is represented by its interactions with CDC28 at different stages of mitotic cell cycle. The chromatin-remodeling complex is assembled when its dynamic component, ARP7, is periodically expressed in S phase to function in chromatin remodeling, which could reflect the just-in-time assembly of protein complexes. In conclusion, the study of decomposing the aggregated network and characterizing the hubs in decomposed sub-networks is useful for further understanding the dynamic functions of yeast cell cycle.