Chapter 3 - Feedforward loop Flashcards
What is a subgraph?
A motif with more than 2 pariticpating elements.
In a random network what is the standard deviation?
the square root of the mean.
The general structure of a feedforward loop:
X regulates Y and both X and Y regulates Z.
What does a coherent FFL imply?
That the indirect path has the same overall sign as the direct one. (even number of minus arrows)
Other than the presence of TFs in the FFL what else is needed?
Possibly signals activating the FFLs.
What is step like stimulation:
Start with high concentration of X but no signal and then suddenly introduce signal.
What is T_ON?
It is the delay in the coherent FFL 1 between the activating X signal and Y reaching a level that makes production of Z possible.
In the C 1 FFL AND what happens if Yst = K_YZ?
In this case T_ON converges toward infinity. This means no activation of Z production.
What is the purpose of of the C1 FFL AND gate?
1) Introduces a delay
2) X activation fluctuations are filtered out (persistence detector)
What is a sign sensitive delay?
Analogy elevator door: doors open immediately when you put something between doors, but brief periods without obstruction are filtered away.
In FFL: you need to have a prolonged period of Xs (no door obstruction) to start closing the door.
What is the purpose of the C1 FFL OR gate?
1) Filters away off signals on Sx and Sy.
What is the purpose of the I1 FFL AND?
1) Generates pulses: when it starts out Z is produced but once Y is generated Z is no longer produced.
What is the purpose of I1 FFL AND where it does not completely shut off Z production?
1) tocreate a rapid start fase (before Y is at active levels) which has a lower steady state (when Y activates).
Name 3 ways of increasing response time:
1) Increase degredation rate (T_1/2 = log(2)/alpha) - beta has to be increased if steady state needs to be the same (Yst = beta/alpha).
2) NAR - can only work for transcription factors.
3) Incoherent FFLs with supression that only hinders production.
What is a biphasic response?
For I1 FFLs When we consider different values for Sx we can get a biphasic response. This means that the system has a high Z at some Sx values and low for other Sx values. This is down to the fact that X activates/represses Y and Z at different tresholds.
