understanding topGO enrichment
I am trying to understand how topGO decides a GO term is enriched. Specifically, I am trying to understand how terms not in my list (universal or my genes of interested with annotated GO terms) can be considered significant.
Like the example below. That GO ID is not in any of my lists, so how is it significant?
GO.ID Term Annotated Significant Expected classicFisher
GO:0009235 cobalamin metabolic process 1 1 0.03 0.02536
Thanks, Mike
• 3,219 views
•
link
written
by
michael.steffen •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How do I extract the p-value from runTest() in the TopGO package?
written by ktm •
-
topGO analysis "MF" term error
written by sim.j.baum
-
topGo analysis getting same number of Annotated, significant and expected
written by rashmi.jain20 •
-
TopGO KS test,0 significant hit but rank ahead?
written by Liyo •
-
Visualisation of GO Terms
written by dthorbur
-
GO Analysis Clarification using GOstats using hyperGTest()
written by brismiller •
-
topGO: GO terms but no P-value score
written by khhgng
-
Getting topGO to work with inverselist GO2geneID
written by michael.steffen •
-
Errors when extracting significant genes per GO.id from topgo data
written by tiago211287
-
Can't find GO annotation with topGO
written by bvernot •
My guess would be that GO:0009235 is a parent term inferred from one of the terms annotated for your genes.