Comparing two RNA-seq data sets mouse and human

Question

[Ahmed.waraky]

Hi I have a question. We have two RNA-Seq data sets one from mouse and one from human for our gene modification, and we wanted to know how similar they are from each other. I know i can convert the mouse gene names to human orthology using tools like Biomat, but how to compare between the two sets after? Do i use Wilcoxon test? Or rank the LogFC and use spearman correlation? Or i merge the two data sets based on gene names?? Thanks for the help!!

Answer 1

[qmarulfiz]

~Must have something to do with using GSEA. Though im not an expert and will be interested also to know how.

Answer 2

[swbarnes2]

I think what's best is to leave the genes as they are, and examine the pathways changed. Hopefully comparable pathways will be changed in both species

[Ankit]

You can upload your differentially expressed genes separately from mouse and human data in gProfiler2 and observe the common biological process affected.

[Ahmed.waraky]

Yes i did similar thing with Gene ontology pathway name and run a script for common pathways. But was curious if there was a way to do that on the gene names

[Ankit]

I doubt gene name would be a good idea to do. Same gene symbols in mouse (eg. Xxxx) and human (eg. XXXX) can have different function (or not exactly same function), conserved sequences and protein encoded. Until you are sure about the gene of interest, it is difficult to compare among the species for prediction. Focusing on outcome like biological process / pathway could be another approach.

May be you can explain your question in detail or your project to understand better.