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SysBioChalmers / Mouse-GEM

Genome-scale model for Mus musculus
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no gene association found in xml model #24

Closed Kai6662 closed 1 year ago

Kai6662 commented 1 year ago

Description of the issue:

Error in loadGSC("/mnt/workspace_dierickx/kcui/mouse-gem/Mouse-GEM/model/Mouse-GEM.xml") : no gene association found

Hi,

I am using mouse-GEM model. I load xml file using loadGSC function in R. But there is no gene association found.

Do you know what is the problem?

Thanks in advance.

Kai

haowang-bioinfo commented 1 year ago

@Kai6662 thanks for reporting this

Please describe your OS environment, software package, so that we can look into it

Kai6662 commented 1 year ago

Hi,

My OS environment is SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux; my software is R; and the package is piano. Piano package can do reporter metabolites analysis using Model.xml. Then I tried to load mouse.xml using loadGSC function.

Best Kai

haowang-bioinfo commented 1 year ago

may I ask if the loadGSC function is to open a genome-scale model?

Kai6662 commented 1 year ago

Based on piano vignette, loadGSC function is to load a gene set collection from a genome-scale metabolic model. It looks like the function included open the model and collect gene set.

haowang-bioinfo commented 1 year ago

I'm afraid this function cannot open a model. Maybe contact piano support to figure this out

mihai-sysbio commented 1 year ago

Based on the documentation of loadGSC, in principle loading a model should work. So I'm wondering now if perhaps it has to do with some implicitly expected gene annotation.

Kai6662 commented 1 year ago

Do you know some alternative reporter metabolites analysis tools? So that I can use your mouse-GEM model well. I only knew piano can do that.

haowang-bioinfo commented 1 year ago

sure, we'd like help

Kai6662 commented 1 year ago

Could you recommend me a software to do reporter metabolites analysis using your mouse model? I would appreciate it.

haowang-bioinfo commented 1 year ago

I think piano is good for reporter metabolites analysis.

To extract GSC from MouseGEM, you may try the following code and this repo:

# Load MouseGEM from your local computer after cloning the repo
load('../Mouse-GEM/model/Mouse-GEM.mat')

# Extract MouseGEM GSC after cloning and installing the GeneSetAnalysisMatlab repo
extractMetaboliteGSC(model, true, 'mouseGSC.txt')

Then the "mouseGSC.txt" file can be used with piano for downstream analysis.

Kai6662 commented 1 year ago

Thank you so much! It is working!

haowang-bioinfo commented 1 year ago

good to know :-)

haowang-bioinfo commented 1 year ago

feel free to reopen