Relations used in GO.db GOBPANCESTOR
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max.neal • 0
@maxneal-20732
Last seen 17 months ago

I'm wondering - what relations does the GOBPANCESTOR function in the GO.db package use to collect the ancestors of a given GO:BP class? Is it just the is-a relations, or does it include part-of and/or regulatory relations as well?

GO.db • 170 views
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@james-w-macdonald-5106
Last seen 6 hours ago
United States

It includes all of those:

library(GO.db)
library(DBI)
con <- GO_dbconn()
table(dbGetQuery(con, "select * from go_bp_parents;")$relationship_type)

                is_a negatively_regulates              part_of 
               57509                 2813                 5388 
positively_regulates            regulates 
                2796                 3240 

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Thank you! That squares with what I'm seeing in my analyses.

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