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:
- https://github.com/biobakery/humann/blob/3.0.0-alpha/humann2/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
- https://github.com/biobakery/humann/blob/3.0.0-alpha/humann2/data/pathways/metacyc_pathways_structured_filtered
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.
Hi franzosa,
I’m new to this forum, please let me know if i’m not allowed to post questions under other people’s posts, i would create a new post instead.
With your helpful answer above, i manage to find the linkage between gene families and pathways. But just one more quick question here:
How does huamann2 associate UniRef*_unknown gene families with pathway abundance?
Looking forward to your reply and thanks in advance!!
Best,
Ben
Replying is allowed and encouraged if you think the reply is related. 
UniRef*_unknowns are genes that didn’t have any matching annotations in UniProt (including EC annotations, which are used to connect to reactions and then pathways), hence they don’t contribute to pathways.
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