Dose/EnrichDO - General Questions

Question

[Zaein]

I do not think code is necessary as I do not have any problem running any of the functions in the DOSE or Enrichmap libraries. I simply have questions about interpreting the table generated by the EnrichDO function.

These are the sources I have read through. However, I am still uncertain if I am understanding things correctly:

1. https://yulab-smu.top/biomedical-knowledge-mining-book/enrichment-overview.html#ora-algorithm
2. ClusterProfiler : What is GeneRatio and BgRatio?
3. https://hiplot.com.cn/books-static/clusterprofiler-book/chapter12.html#pathview-from-pathview-package

When I run the EnrichDO function I get a table as expected.

GeneRatio (k/n): k is the number of genes from my geneset that were found for a given DO term. n is the number of genes from my geneset that were present in the DO database.

BgRatio (M/N): M is the number of genes from my geneset that are directly or indirectly related to the DO term. N is the number of genes from the organism I am importing from (i.e, org.Hs.eg.db) that were found in the DO database.

Also, is there a way to retrieve a list of genes that compose n, M, or N?

Cheers,

[jwil14]

Hi, I'm also struggling with an aspect of this. I can't understand how the ranking of the pathways to be plotted using enrichplot are determined. I've plotted the dotplot successfully, but the pathway with the lowest p value and highest GeneRatio is not included in the dotplot for some reason. Is it because BgRatio is also taken into account? Many thanks for your help.

[Zaein]

Can you add pictures to illustrate things? The dot plot and the pathway in question in particular.

[jwil14]

The top 7 results plotted in the dot plot:

[jwil14]

Results file ranked by GeneRatio

[jwil14]

Results file ranked by p-adjusted value

[jwil14]

It doesn't make sense to me that Extracellular matrix organisation would be at the top of the dot plot when it doesn't rank at the top for either p-adjusted value, GeneRatio or Count. It makes me think that it much be based on GeneRatio but also taking into account BgRatio?

[Zaein]

I can't see your entire dot plot but I think I can still help you. We can choose what gets plotted in the dot plot by doing something like this...

categories <- c("Phase 1 - Functionalization of compounds", "Collagen Chain trimerization", "Xenobiotics")
dotplot(df, showCategory=categories)

Does that help?

[Zaein]

I am still looking for answers :)