A comparison of the functional modules identified from time course and static PPI network data

Xiwei Tang, Jianxin Wang, Binbin Liu, Min Li, Gang Chen, Yi Pan
2011 BMC Bioinformatics  
Cellular systems are highly dynamic and responsive to cues from the environment. Cellular function and response patterns to external stimuli are regulated by biological networks. A protein-protein interaction (PPI) network with static connectivity is dynamic in the sense that the nodes implement so-called functional activities that evolve in time. The shift from static to dynamic network analysis is essential for further understanding of molecular systems. Results: In this paper, Time Course
more » ... tein Interaction Networks (TC-PINs) are reconstructed by incorporating time series gene expression into PPI networks. Then, a clustering algorithm is used to create functional modules from three kinds of networks: the TC-PINs, a static PPI network and a pseudorandom network. For the functional modules from the TC-PINs, repetitive modules and modules contained within bigger modules are removed. Finally, matching and GO enrichment analyses are performed to compare the functional modules detected from those networks. Conclusions: The comparative analyses show that the functional modules from the TC-PINs have much more significant biological meaning than those from static PPI networks. Moreover, it implies that many studies on static PPI networks can be done on the TC-PINs and accordingly, the experimental results are much more satisfactory.
doi:10.1186/1471-2105-12-339 pmid:21849017 pmcid:PMC3174950 fatcat:tz4hhurihfbp3i24of67aohipy