How to look for enrichment of pathways using a list of EC numbers (enzyme)?
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7 months ago
O.rka ▴ 300

I ran PICRUSt2 on a human microbiome and ran some statistical tests on different enzymes for different phenotypes. I have a list of 81 enzyme numbers and I want to see if there is any enrichment in any higher level categories such as nitrogen metabolism.

Is there any way to do this?

enzyme enrichment gsea picrust gene set • 332 views
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You may be able to use the ec2path, ec2go, pathway.info files in the Fun4me package:

https://sourceforge.net/p/fun4me/code/ci/master/tree/data/

You can also use the Minpath tool, or use the whole package!

More info: https://link.springer.com/protocol/10.1007/978-1-4939-7015-5_3

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