We have done microarrays for wildtype-control treatment, wildtype-toxin treatment, mutant-control treatment and mutant-toxin treatment.
The goal is to find diffferentially expressed genes regulated by toxin in wildtype and then find out which of these regulation are mutant dependent.
The first goal is typical. So we did SAM and limma. Both could give us a bunch of DEGs. However, I am lost about getting the second aim done.
With limma and 2x2 factorial analysis, we could find the DEGs from all kind of pairs, such as wildtype -Toxin/control (this answers the first goal) or mutant/wildtype in control treatment (this tells us how the mutant gene is affecting the basal expression without toxin).
But I don't know how to find the wildtype DEGs which have regulation depending on the mutant gene. Say one gene is up-regulated 100 folds by toxin (i.e. toxin treatment/control treatment) in wildtype. Then if this gene is up-regulated 3 folds (toxin treatment/control treatment) in mutant, it will be apparently mutant gene dependent (from 100 folds in wildtype to 3 folds in mutant). However, this gene will be shown as DEG in the mutant analysis as well since it is more than the 2-fold cutoff. Then if I only compared the DEGs in different pair of analysis from limma, I will miss these kind of genes. There must be some dedicated way to analyze this but I could not find it. Any suggestion will be appreciated. Thanks a lot.