Why does XomicsToModel remove the intermitochondria compartment

[Juan Sepulveda]

Hi all,

I am working with XomicsToModel, and I noticed that my contextualized models had very high flux through ATPS4minew, a reaction created by XomicsToModel after removing the intermitochondrial compartment. However, this means ATP can be produced by adp[m] + pi[m] + h[m] without input from the canonical ETC reactions. I noticed that the intermitochondrial compartment is removed by XomicsToModel when ThermoKernel is used as the tissue extraction algorithm, and I would like to know why this is the case.

Thank you,

Juan

[Ronan M.T. Fleming]

Hi Juan,
in fairness, this is an area that needs more attention, e.g., to
systematically represent the spatial localisation of all
mitochondrial-associated reactions in more mitochondrial compartments
than is currently the case. When you say that "ATP can be produced by

adp[m] + pi[m] + h[m] without input from the canonical ETC reactions"

what method did you use to predict the flux? It is assumed if you are
using thermoKernel that you follow up flux predictions with a
thermodynamically feasible flux prediction method. There are several
already implemented in the cobra toolbox reviewed here
https://arxiv.org/abs/2607.25217 and more to come.
Regards,
Ronan

> --
>
> ---
> You received this message because you are subscribed to the Google Groups "COBRA Toolbox" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to cobra-toolbo...@googlegroups.com.
> To view this discussion visit https://groups.google.com/d/msgid/cobra-toolbox/95e31f42-d41e-4671-a969-789ae20d9ab3n%40googlegroups.com.



--
--
Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
----------------------------------------------------------------------------
Associate Professor,
Digital Metabolic Twin Center, www.digitalmetabolictwin.org
& School of Medicine,
& Institute for Clinical Trials,
University of Galway.
Ireland.
----------------------------------------------------------------------------
Coordinator of the Horizon Europe project "Reconstruction and
Computational Modelling for Inherited Metabolic Diseases" (Recon4IMD)
----------------------------------------------------------------------------
Peer-reviewed publications: https://goo.gl/FZPG23
Mobile: +353 852 109 806
Github: @rmtfleming
----------------------------------------------------------------------------