Unlike feature / compound level analysis, we don’t explicitly compute if a pathway is enriched in one group compared to other group. The name is misleading, a better term is if a pathway is perturbed. In real experiments, metabolites in a pathway can be either up- or down-regulated due to dynamic regulation of metabolic flux. They are very meaningful.
You can always see the actual compound-level concentration changes in MetaboAnalyst (click the View link) as shown by the Figure below
Thank you for this explanation. However, In some cases (see example below), the enrichment analysis suggests one pathway being significantly perturbed, but the individual metabolites within that metabolite set are not enriched in the same direction. How can I know which whether the pathway is more perturbed/enriched in one group versus the other?
The perturbed / enriched status of a pathway is calculated by comparing metabolite concentration profiles between two groups (one of them is considered reference), we then rank different pathways by their p values.
To answer your question, we need to have a third reference (normal) baseline concentrations of each metabolite in a pathway, then compare each group to that baseline profile.
Thank you for your reply. How can I determine which of the two groups is considered reference? I tried changing the labels of my two groups, but the result always stays the same. If one of the groups is considered a reference, then we should be able to identify in which group the pathway is more or less perturbed compared to the reference?
The tool gives you the information, and you make the decision regarding the question you asked.
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