How to integrate the transcriptomics data with kinetic metabolic models?
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22 months ago

I have created a convenience kinetics model. Now, I want to integrate the transcriptomic data with my convenience kinetics* model for altering/weighing the kinetic parameter values. I read some publications a bit similar to this work but couldn't get any proper idea of doing it in the right way.

Details: I've got a pancreatic model for the study on type 2 diabetic patients. It has few compartments, the reaction pathways, and the species are metabolites. All the reactions are convenience kinetics based. Enzyme is a constant factor, so its production and regulation is not considered. From my model, I'll get the Vm values for all the reactions and then I'm supposed to get the Vm(Vmax of MM kinetics) values for the type 2 diabetic patients by somehow integrating the transcriptomics data with it. I was asked to use the fold change values and all. But I couldn't get any relevant publication and without proper guidance(my PI has suggested me these but hasn't worked in this area before), it's really difficult to proceed.

Any leads or pipelines will be highly appreciated.

*(You can call convenience kinetics rate laws as approximate rate laws or you might have heard about "modular rate laws", they are more or less the same. We use this approximate rate law approach in cases where we don't have the experimental data for all the true rate law parameters. If you want to know more about Convenience kinetic rate laws, here's a link to a good publication )

systems-biology proteomics transcriptomics gene • 302 views

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