P-value in Pathway analysis for data with two groups

I’m struggling to understand the p-value from enrichment analysis that are done while running pathway analysis in MetaboAnalyst. What significance does these values represent? Especially, when you upload the data for metabolite concentrations for two groups, what these p-values are? Are these the comparison between two groups e.g., a given pathway significant in one group compared to the other? If yes, how the software decide reference group? Please elaborate so I can understand this part. Thank you in advance.

Please note that all our methods are published and documented. For this general question, I would suggest you to read our paper first . We will be happy to answer more specific questions. Here is also a related question on this topic.