I'm trying to test out and understand HUMAnN2's pathway abundance output.
What I'm looking to do is see how well HUMAnN2 does in metabolic pathway analysis. To do this, I have a list of ECs from an external source, and I want to run it through HUMAnN2's pathway abundance analysis.
The list of ECs have an associated abundance score. However, the documentation surrounding the formation of the pathway abundance output is murky.
I have the EC -> metacyc reaction (A), and metacyc reaction -> pathway (B )maps.
I was originally taking all entries in map B, and summing up all EC abundances associated with the pathway, and calling this result the "pathway abundance". Is this wrong?
According to the literature, I should be doing something different but I'm not sure.
-> reconstruct the pathway, and check to see if the reactions I've got satisfies any of the pathways
-> Then using the abundances of the reactions, the pathway abundance is going to be the lowest amount
eg: Pathway 1 has reaction A, B. A is 15, B is 5. Therefore, pathway 1's abundance is 5
Additionally, if pathway 1 has alternate definition: reaction C, D. C is 10, D is 15.
Pathway 1's real abundance is 15, from 5 (A and B ) + 10 (C and D)
If I could just insert the ECs into HUMAnN2's existing workflow, this should solve my problems, and I can avoid reverse-engineering the code.
Does anyone have an opinion, or experience in the matter?