XuhangLi
commented
1 year ago Hi,
Very good question. The answer is yes and no…
Assuming what you mean is that your biomass function is not in the solution space (NSLS), this problem is usually caused by some lowly/rarely expressed genes in your input dataset that are actually essential for making biomass. If you can easily find the candidates, and manually move them into moderately expressed gene category, the problem will be solved.
However, it can be time-consuming to identify the bottleneck genes, or different conditions may have different genes. One workaround is to use the idea of ‘core reactions’ that used to be implemented in the original iMAT algorithm. You can define a set of essential reactions for biomass objective, then add them to the ‘core reaction’ set such that they will be considered as ‘active reaction’ regardless of the gene expression of their associated enzymes.
Unfortunately, we don’t have the ‘core reaction’ function implemented in current iMAT++. However, this function has been implemented in a follow-up study that we are going to post onto bioRxiv soon. You may expect this to be available in a few days to weeks.
If you have urgent needs, I recommend tuning the gene category. In our experience, such problem can be simply caused by the unexpected low expression of one or two genes. An easy fix would be to put these genes always to moderately expressed category regardless of their gene expression.
Hope this could be helpful!
Thanks, Hang
From: kamoors @.> Date: Tuesday, November 8, 2022 at 7:39 AM To: WalhoutLab/MERGE @.> Cc: Subscribed @.***> Subject: [WalhoutLab/MERGE] Exclusion of biomass reaction (Issue #6)
Hi!
I am using iMAT++ to create a model based on RNA-seq data, but for some of my treatment models, the algorithm sets the biomass function as inactive.. Is there a way to make this reaction always active in all runs?
Thank you!
kamoors
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Hi!
I am using iMAT++ to create a model based on RNA-seq data, but for some of my treatment models, the algorithm sets the biomass function as inactive.. Is there a way to make this reaction always active in all runs?
Thank you!
kamoors