Functional categorization of pathways

Microbial community profiling HUMAnN
1

Hi team,
Thank you for the great tools !

I am currently working with my pathway_abundance (unstratified) data output from HUMAnN3. Instead of listing significant pathways in isolation, I wanted to categorize them based on their biological roles, such as Metabolism (Carbohydrates, Amino Acids, Lipids), Biosynthesis (Vitamins, Coenzymes, Secondary Metabolites), Energy Production (Oxidative Phosphorylation, Fermentation), or Pathogenicity (Virulence, Antibiotic Resistance). I was wondering if there is a way to generate or access a pathways-to-categories.tsv file that would allow me to do this for my pathway abundance data.

Any help or guidance in this matter would be greatly appreciated.

Thanks!
Santosh

2

If you search the forum I think there are a few different ways users have imposed a level of organization above the MetaCyc pathways (similar to what you described), including a version supplied by MetaCyc itself. It’s not something we officially bundle with the HUMAnN software.

1 Like
3

Hi @franzosa,
Noted. Thank you for your suggestions.
Best,
Santosh