Enrichment VS singletons

[Sirbius]

Hi guys,

I run a Pangenome analysis on Pseudomonas strains, identified the core, accessory and singletons gene clusters.

When I run the enrichment I found that one group (containing only one individual) is enriched in, for example, 10 gene clusters. However, these 10 gene clusters do not correspond to the singleton gene clusters of that individual!!
Whad did I not get? 

I thought I would have ended up with the same results/gene clusters..

Hope someone can explain this to me,

Thanks,

Silvia

[A. Murat Eren]

How many genomes do you have in that pangenome?

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[Sirbius]

Hi Meren,

Very few, 21 in total arranged in four different groups (according to pathovar or geographic origin).

Do you think it would be not significant?

[Alon Shaiber]

Hi Silvia,

If I understood correctly, one of your groups has a single member. Please notice this warning from the pangenomics tutorial (

https://merenlab.org/2016/11/08/pangenomics-v2/#making-sense-of-functions-in-your-pangenome):

“ Our example here includes only two categories (LL and HL), but you can have as many different categories as you want. Just remember that if some of your groups have very few genomes in them, then the statistical test will not be very reliable. The minimal number of genomes in a group for the test to be reliable depends on a number of factors, but we recommend proceeding with great caution if any of your groups have fewer than 8 genomes.”

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[A. Murat Eren]

Gene clusters that are occurring in only one of 21 genomes can't be assumed to be 'enriched' in any group. The purpose and the details of the enrichment algorithm is explained here: 

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02195-w

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[Sirbius]

OK guys, got it. 
Thank you very much!

Silvia