Mouse single cell data

[gaelcge]

Dear dev
Any direction you can point toward to analyse mouse tissue single cell data?
Thanks
Gael

[qaz-94]

In our study, we utilized METAflux, which is based on the human metabolism network. It's important to note that mouse metabolism can vary from human metabolism. In our manuscript, our analysis focused on CAR-NK cells in a xenograft model. Therefore, while exploring using mouse data within this context might be feasible, you just need to convert the gene names, but it's essential to proceed with caution due to potential metabolic differences between species.

[GilbertHan1011]

Do you have plans to use it for the Mouse later on? If so, it will be a great help.

[RestlessTail]

Dear Authors,

I’m exploring the possibility of reconstructing a mouse-specific GEM using an SBML file from Metabolic Atlas and replacing key variables in METAFlux. Based on my understanding:

gene_num maps gene IDs.

iso represents gene associations with OR logic.

simple_comp represents gene associations with AND logic.

multi_comp represents mixed OR/AND gene associations.

Hgem$LB and Hgem$UB are lower and upper bounds.

Hgem$Reaction is the reaction ID, Hgem$pathway indicates the reaction type, and Hgem$rev denotes reversibility.

Hgem$S describes reactions using 1 and -1 for products and reactants, but I’m unsure how the columns map to specific compounds.

Hgem$Obj is unclear to me.

Could you confirm if my understanding is correct and clarify the roles of Hgem$S and Hgem$Obj? Additionally, would this approach be feasible for creating a mouse-specific GEM?

Thank you for your time and guidance!

[RestlessTail]

I’ve developed a converter prototype called SBML2Flux to adapt SBML files for use with METAflux. While I’ve primarily tested it on mouse data, the tool should, in principle, be compatible with other species as well. To keep this thread focused, I’ve documented the conversion process in the tool’s README.

The tool has performed well on my dataset, but I would greatly appreciate your feedback on whether this approach aligns with the intended design of METAflux. Your insights would be invaluable in ensuring the tool meets the needs of the community.

Thank you for your time and guidance!