I am PhD student and im working on a non-model organism trying to understand the differences in expression patterns and differentially expressed genes between resistant and susceptible responses .
I have 3 species (quite similar) infected with two different strains of a pathogen, some are susceptible and others resistant? I want to mainly understand the genes involved in defense & susceptible responses. The approach was to compare the orthologous genes across the three species. now i have a table with the gene expression values for each replicates (*3) in different treatments and log2FCby comparing to the mock and treatment of each responses.
Is there any idea that someone could provide on how do i select the top candidates for defense responses and the highyl differentially expressed genes during susceptible interaction from this table ??
any suggestions/inputs will be super helpful.