Module preservation between multiple species

[FraMont2]

Dear smorabit,

Thank you for developing such an amazing R package!

I am particularly interested in the cross-species analysis functionality and have a few questions about this:

1. From the tutorial, I see that you use the hg38_mm10_orthologs genes for projecting modules. My question is: Should I identify co-expression modules in human using only human-mouse orthologous genes and then project these modules onto mouse orthologous genes to maintain consistency in the analysis?

2. I am working with data from 9 species, where the total number of orthologous genes across these species is approximately 9,000. In your experience, is it reliable to identify co-expression modules using fewer than 50% of the total annotated genes?

3. My goal is to identify co-expression modules that are conserved across all 9 species. How would you recommend running module preservation analysis across multiple species? I am considering the following approach:

• Identify co-expression modules in species A using the ~9,000 orthologous genes.
• Project these modules from species A to species B.
• Sequentially project modules from species B to species C, and so on for the remaining species.

Does this approach sound appropriate, or would you suggest an alternative method?

Thank you in advance for your time and insights!

Best,
Francesco