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View Code? Open in Web Editor NEWepigenome scale metabolic modeling for cancer metabolism
License: MIT License
epigenome scale metabolic modeling for cancer metabolism
License: MIT License
ISSUE WITH SOME METABOLIC REACTIONS
Some metabolic reactions that are expected to output a flux value return 0 in the metabolic_sensitivity.m
code.
To Reproduce
Steps to reproduce the behavior:
run_all.m
to line 145Steps for drug sensitivity analysis:
Validation steps:
Next steps:
Describe the bug
The reduced cost line in metabolic sensitivity returns an output error. The value that I want stored (which in some cases is 0) is returned as an empty array. This causes a size error.
To Reproduce
Run the code as written in the scampit branch
Expected behavior
I would expect that the empty value will be filled in as a 0 if the reduced cost were in fact 0.
Examples of other acylation reactions
Things to do:
Now that you have extracted more genes that correspond to histone writers and erasers, there are several more tasks we can do for more in-depth analyses:
These reactions have leaks - need to resolve them.
The RxnGeneMat does not accurately map genes and reactions, probably because old identifiers are used. Need to fix this now.
To add these metabolic nodes, I need to look for literature evidence about
Lauren:
Scott:
Later...
Fill metabolic map and write code to add reactions RECON1 using metabolic map as an xlsx or txt file.
Scott:Get both acetylation and methylation cases
Lauren: methylation cases are a must, acetylation is optional
To pick up later:
Describe the bug
@ScottCampit did not add some medium components, as there were few cell lines that were grown in the medium conditions, and the amount of glucose in the medium was similar to another medium condition. However, it is now apparent that these assumptions do not hold, and I need to finally fix the medium conditions.
To do:
I wrote code that outputs the metabolic fluxes for various medium conditions in three separate cases. One case uses FBA as the optimization method for calculating the metabolic fluxes. However, from Shen et al., 2019, the output does not match.
To test:
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