The bioBakery help forum

Is "pathabundance" associated with "genefamilies"?

Hi, I want to know which genes are in a specified pathway that I get from the “pathabundance” table. How can I get this infomation? Is “pathabundance” associated with “genefamilies”?

Many thanks.

Yes - we compute pathway abundance from reaction abundance, which in turn is computed from gene abundance. Within the HUMAnN installation there is a file that maps UniRefs to reactions and another file that defines pathways as collections of reactions:

You could use these to work backward from your pathways to see which genes might’ve contributed to their abundances.

Thanks. I will try it and let you know th eprogress.