Do genes have to come from the same species in pathway identification? For example, Pathway X requires Gene 1 and Gene 2 to come from Species Z to count as a valid pathway hit?What happens if Gene 1 is from an unclassified species and Gene 2 is from another unclassified species. Would Pathway X still show up in the results?
--
You received this message because you are subscribed to the Google Groups "HUMAnN Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to humann-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/humann-users/f4985fe7-71b7-49db-aa5e-2ca48a253ece%40googlegroups.com.
Hi Nick,Community-level pathways (i.e. the ones in the output that aren't followed by "|species" or "|unclassifed") are quantified from community-total abundances. Hence, they could represent a mixture between components from different species, known or unknown. Pathways in the "unclassified" stratum are similarly computed from "unclassified" reaction abundance, which could be coming from one or many species.Thanks,Eric
On Tue, Oct 15, 2019 at 2:26 AM Nick <nicochun...@gmail.com> wrote:
Do genes have to come from the same species in pathway identification? For example, Pathway X requires Gene 1 and Gene 2 to come from Species Z to count as a valid pathway hit?--What happens if Gene 1 is from an unclassified species and Gene 2 is from another unclassified species. Would Pathway X still show up in the results?
You received this message because you are subscribed to the Google Groups "HUMAnN Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to humann...@googlegroups.com.
Thanks, just wanted to make sure I wasn't misunderstanding. So if we want to be more conservative and only look at which pathways exists within a single species, we should only consider PathwayX|speciesY.
For community-level and unclassified pathways, does it make from an ecological perspective to construct pathways this way? In other words, would two separate genes expressed by two separate species ever form a pathway in practice? I know many species utilize the metabolites of other species to form certain compounds, but I'm sure there are many reactions that have to occur with a single native cell.