Question: Time steps in node perturbation analysis
gravatar for priya.bmg
9 days ago by
priya.bmg0 wrote:


Why do we specify time steps while performing simulations?. For example, in node perturbation analysis, I perturb Gene A (knock-out) and simulate how this perturbation affects expression of other genes. I do this perturbation for time steps ts=0 to ts=150. How is the result at ts=0 different from ts =150? Do we give more time steps to see how the perturbed gene affects the expression of other genes as the time evolves? What time steps mean in this analysis?



ADD COMMENTlink modified 9 days ago by Joe18k • written 9 days ago by priya.bmg0

Is this a homework question?

If you perturb a system, what does your intuition tell you about why you might want to observe this over an extended time period? There is no such thing as a perturbation fixed in time, a perturbation is only a perturbation relative to some observed behaviour of a system.

ADD REPLYlink written 9 days ago by Joe18k

@Joe Thanks. It is not a homework question. Sorry if it sounded that way. I have always been reporting the regulation of gene expression at the last time step (ts =150). Now, it struck to me then about the previous time steps. Should I take an average of the regulation of gene expression at all the 150 time steps? If I take the average how is it biologically relevant and so what does the time steps mean in the analysis. Maybe at ts =150, we show how perturbation evolves the regulation of gene expression from ts=0 and gets stabilized at the last time step 150. For example, at time step 0 Gene B is upregulated 50%, then gradually increases and gets stabilized and there is 100% upregulation of Gene B expression at time step 150.

ADD REPLYlink written 8 days ago by priya.bmg0

It depends what the exact question is that you're asking?

If the question is "how does expression of gene x differ at t=150, from t=0 then you just describe the state change.

If the question asks you how the system has evolved in this time period then you will want to look at the shape of the curve, perhaps the rate of change etc.

Average expression doesn't strike me as that informative but again it depends what the question is.

ADD REPLYlink written 8 days ago by Joe18k

Thanks. The question is "how perturbation (knock-out) of gene A affects a gene B expression". I will show the shape of the curve to show how the system evolves in response to the perturbation from time step t = 0 and t =150. I have been thinking and yes you are right average expression doesn't seem to answer any question.

ADD REPLYlink written 7 days ago by priya.bmg0
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