Confusion Regarding Metabolite "Expression" in OmicsNet.ca

[nghia.pham]

Hi everyone,

I’m encountering some confusion while performing a multi-omics analysis using OmicsNet.ca, where I’ve integrated both metabolomics and transcriptomics data. During the processing, I selected the “metabolite-protein interaction” option for both omics layers, and the platform generated an interaction network that includes the genes and metabolites I provided.

However, I noticed an issue: while the “expression” values for the genes in the transcriptomics data seem to align with their log2 fold change (log2FC), the “expression” values for the metabolites appear inconsistent. In some cases, metabolites with negative log2FC in my original data are shown with positive “expression” values in OmicsNet’s network.

I’ve looked through the tutorials and forum but couldn’t find an explanation of how the “expression” for metabolites is calculated or what algorithm is used. Has anyone else faced this issue or can help explain why this happens? I’m unsure about using these results since I don’t fully understand how the data is being processed.

Any help would be greatly appreciated! Thanks!

[jeff.xia]

Please carefully read and follow our post guideline.

For your question at higher level, OmicsNet does not compute “expression” values for any features. The general input is a list (IDs) - the 2nd column (optional) is for “expression value” if you call it. Its sign or interpretation is only meaningful to the users who provide the value