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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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Question: Meaning of fold enrichment #120

Closed dalhoomist closed 2 years ago

dalhoomist commented 2 years ago

Thank you for this wonderful tool.

I sometimes get fold enrichment results that are less than 1 - typically 0.7-0.8 - still significant though. If I understand the documentation and your paper correctly, the pathways with fold enrichment less than 1 should be under-represented in my dataset. Is that correct? If so, why is not common to see random pathways being under-represented?

Kind regards

egeulgen commented 2 years ago

Hello,

Thank you for using pathfindR.

Below is the description for Fold Enrichment:

Fold Enrichment: Fold enrichment value for the enriched term (Calculated using ONLY the input genes). This is calculated as the proportion of pathway genes within all INPUT (not subnetwork) genes over the proportion pathway genes within the background genes. For example, if the proportion of pathway genes in the input is 0.5 and the proportion of pathway genes in the background is 0.25, the fold enrichment value is 2. The background genes in pathfindR is used as all the genes in the protein-protein interaction network.

Because the enrichment tests are performed on active subnetworks and not input genes, it is possible to have a FE value < 1. This simply indicates that while there is under-representation in terms of input genes, the respective active subnetwork, containing the relevant input genes as well as inter-connecting genes from the PIN, is enriched for the given gene set.

Hope this helps, -E

dalhoomist commented 2 years ago

Thanks so much! Really helpful.