Joint pathway analyses and fold change

MetaboAnalyst
1

I am using joint-pathway analysis with metabolomics and proteomics data, both with and without Fold change values added. Surprisingly, Fold Changes are not considered in calculations and the pathway statistics values given are the same with and without fold change values (thus, FCh seems to be completely dispensable?). Thanks for feed back

Enrique Gomez

2

This is correct.

  • The fold changes or p-values are already used in selecting those significant features. The joint pathway analysis only considers presence or absence (i.e. hits).
  • Directionality in pathway analysis are not considered, as we are not aware any validated methods on this (please feel free to share any related publication if you know). We do offer visualization support that will color the nodes/edges (compounds or proteins) based on FC to indicate up- or down- regulation.
3

Thanks for your kind, quick reply.

Whether the FCh values need to be filtered before running joint pathways, and as seen in the Metaboanalyst 6.0 site examples, there is no convenience in using sample values that include a FCh value over those that do not.

Best regards

Enrique

4

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5

Hello Enrique,

I have added support for coloring metabolites and enzymes by fold change colors, you can give it a try!

Cheers,

Guangyan