I have a question. I want to perform over-representation analysis on GO terms associated with my list of significant genes and get KEGG pathways. I saw there are two tools I can use in R: clusterProfiler and gProfileR. Are they the same? Am I going to get the same results from the two? if not, what is the difference? and why?
Thank you!
1 answer
The basic principle is similar but each tool has their own way of defining background genes and calculating enrichment stats + multiple testing correction. In my experience this entire world of gene enrichment analysis is a gigantic mess. It is not standardized, results drastically change upon slight changes of the input gene lists and there is no consensus on what (if at all) should be used as a backgrounf set of genes to calculate enrichment over. Gprofiler2 allows to define a custom set of genes as background, so that is a plus, not sure whether the other tool can do that.
Log in to answer this question.
-
No over-represented GO terms, but plenty from GSEA?
written by bioinfo2345 •
-
gProfiler vs Panther_go in overrepresentation pathways R analysis
written by tchosange •
-
Over-representation Gene Ontology Analysis on Subset of DE Genes
written by lucia.liu54 •
-
GO and KEGG pathway analysis of lncRNA genes
written by basuanubhav •
-
is it meaningful to enrich an organism using ontology from a different organism?
written by anonym101
-
How to make a plot with gProfileR results?
written by Biologist
-
GSEA related to other functional analyses
written by sup230 •
-
Best UPDATED tool for enrichment anlysis
written by ncl.lazzarini
-
KEGG pathways associated to a gene using BiomaRt
written by TitoPullo
-
Pathway Over-Representation Across Multiple Gene Lists
written by Obi Griffith
https://hbctraining.github.io/DGE_workshop/lessons/functional_analysis_other_methods.html