This projects fits the parameters of a regulatory network
- mRNA levels can be measured in a variety of ways.
- The same methods can be applied to all sequences.
- Protein levels are much harder to measure
- Mutants give information
- It is possible to determine where on the DNA a transcription factor binds. Likewise to determine if two proteins interact, etc.
- Mutations are useful to: reveal components involved in a system, indicate causality, hint at how things are regulated.
- A/B/C form a loop.
- A activates transcription of B.
- B activates transcription of C.
- A represses B’s activation of C.
- C represses transcription of A.
- C increases degradation of B (which is otherwise slow).
- Other components are degraded by dx/dt = -kx.
- D is regulated by A, B and/or C but the relationship is unknown
- Hill coefficients in the system are small integers (1 or 2)
The network showed in the next figure
The equation system proposed is:
To solve it simmulated annealing and genetic algorithms were applied. An example of genetic algorithms can be found .
The Experimental data that needs to be fit is shown in the figures bellow:
When mD is not considered
When mD is considered
Overexpression mutants, transcription.
Using simulated annealing the results obtained are as follows:
