Adding new reactions to model

[Jin]

Hi

How to add reactions for genes with more than one copy in the chromosome? Are they only added once to the reaction list? Do I need to change their boundaries or anything else to represent their overexpression effect?

I also want to add genes that are not-native to my microorganism and have different names but they do similar reaction as in native condition, but with different enzyme kinetics. Can I only add a new GPR to the native reactions?

Many thanks in advance.

Jin

[Thomas Pfau]

Hi,

>
> How to add reactions for genes with more than one copy in the
> chromosome? Are they only added once to the reaction list?

Yes, they are only added once.

> Do I need to change their boundaries or anything else to represent
> their overexpression effect?

That depends on what you plan to do. If you have an algorithm you want
to use that maps gene expression data, the algorithm should take care of
this. If you have a model that is already restricted to certain flux
amounts you will have to decide how to reflect the overexpression.

>
> I also want to add genes that are not-native to my microorganism and
> have different names but they do similar reaction as in native
> condition, but with different enzyme kinetics. Can I only add a new
> GPR to the native reactions?

Adding the additional GPR-Relation to the existing reactions should be
sufficient. For enzyme kinetics it again depends a lot on how you model
them. BY default "normal" FBA does not consider kinetics apart from
reaction directionality, but there are methods to incorporate enzyme
efficiencies (even though I don't think they are implemented in the
toolbox yet, but I might be wrong here.

Best

Thomas

[Jin]

Sorry, I am new to this field. I don't have the expression data to show the overexpression effect. Can I show the overexpression by setting the reaction boundary at 1000 instead? 

Thanks a lot again!