What computational methods exist or have been used in order to study trans-acting elements in molecular biology.

Question

[Saad Khan]

Hi, apologies for the generality of the question. Trans-acting generally mean acting from a different molecule. It is the opposite of cis-acting ("acting from same molecule"). I am curious as to what computational methods/models exist or have been used to study such trans-acting mechanisms.

[Devon Ryan]

Can you narrow down the subarea within molecular biology for which you're interested in models? Since a lot of things act in trans, there are many models out there. Some of the ones I'm more familiar with are those for the circadian rhythm, which has been numerically modelled a number of times (search pubmed).

[Saad Khan]

Well lets say for example that DNA methylation of one region mihgt be affecting the DNA methylation of another genomic region. How do you computationally predict that or study that.

[Devon Ryan]

That ends up becoming a question of how you measure correlations, to which the answers include linear (or generalized linear, depending on how you do your measurements) models and or any of the large number of machine learning techniques. I should note that it's easier to manipulate things when you have an actual trans-acting element, rather than a region that's affecting something that's presumably then the actual trans-acting element (assuming no long-range interactions, of course).