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I want to compare the results from functional enrichment (e.g GO term enrichment generated by gProfileR) between two gene lists. The idea is to see if these gene lists are enriched in the same terms or if they have specific terms.

This is easy to do at a glance when you have few terms but when the number of terms increases and due to redundancies in GO term annotation a manual comparison becomes unreliable.

So the questions is: Is there a tool for comparing the results from functional enrichment between different gene lists?

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To compare gene list based on gene ontologies you can use GOSemSim (Note, I'm a contributor to the package). You can select the semantic similarity to compare them, that is how the redundancies and hierarchical relations are counted. The main result you can obtain is similarity matrix for each comparison between gene lists.

However if you perform a GO term enrichment and then you compare the gene list of each GO term by looking at which GO do they belong it won't be much useful. I would suggest you to use BioCor (I'm the developer of it), which can use any pathway information (such as the ones of Reactome) to asses if they are related to the same pathways.

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  • $\begingroup$ can biocor use output from enrichr or toppgene? $\endgroup$
    – kcm
    Sep 15, 2019 at 19:27
  • $\begingroup$ @krushnachChandra I think this is a different question. But yes, you can take a list of pathways from enrichr, toppgeene or other enrichment tools and use it as an input (but you'll need also a source of information about those pathways as input too) $\endgroup$
    – llrs
    Sep 16, 2019 at 8:42
  • $\begingroup$ let me try and will update you $\endgroup$
    – kcm
    Sep 16, 2019 at 10:28

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