compareCluster's enrichGO difference in results when stating ont = "ALL" vs NULL

Question

[TIANTHING JESTLIN]

Hi there, I have performed the analysis using the codes below:

compareGO <- compareCluster(geneCluster = gene_lists_sorted_names, 
                            fun = "enrichGO",
                            OrgDb= org.Hs.eg.db, 
                            pvalueCutoff=0.01,
                            qvalueCutoff=0.05)

compareGO<- simplify(compareGO,
                cutoff = 0.7,
                by = "p.adjust",
                select_fun = min,
                measure = "Wang",
                semData = NULL
                )

I had assumed that if setting fun to enrichGO and not stating anything for ont, the default would be "ALL" .

However when I performed:

compareGO <- compareCluster(geneCluster = gene_lists_sorted_names, 
                            fun = "enrichGO",
                            ont = "ALL",
                            OrgDb= org.Hs.eg.db, 
                            pvalueCutoff=0.01,
                            qvalueCutoff=0.05)

compareGO<- simplify(compareGO,
                cutoff = 0.7,
                by = "p.adjust",
                select_fun = min,
                measure = "Wang",
                semData = NULL
                )

The results were different dot plots I obtained from the results were different.

Can I please get some help on understanding this please? Why are the results different?

Answer 1

[Dunois]

compareCluster basically calls enrichGO internally (refer https://github.com/YuLab-SMU/clusterProfiler/blob/devel/R/compareCluster.R#L59 ) which is the function to which the value supplied to the ont argument is passed on to.

If you look at enrichGO's code, you'll see that the default ontology category is MF (ont="MF"; https://github.com/YuLab-SMU/clusterProfiler/blob/devel/R/enrichGO.R#L32). (MF in this case is "Molecular Function"; refer https://geneontology.org/docs/ontology-documentation/ .)

This is presumably what is causing the difference between your runs; I believe you will find your results with ont="ALL" to likely be a superset of the results for ont set to default (i.e., no value supplied).