I plan to work on a toy model extracted from p53 signaling pathway.
This model consists of two parts: 1. An oscillator module with a negative feedback loop, the transcription factor level (p53) can therefore be oscillatory; 2. Gene transcription process with probably feed forward loop or phosphorylation cascade. What I’m interested in is how gene expression level/pattern is controlled by dynamic inputs.
I think I’ll first use Vcell and BioNetGen to implement the model, and explore the feature of the model with XPP as much as I can. Hopefully, this toy model can capture the interesting experimental phenomena in this paper.