RNA seq analysis

Question

[maria]

I wana ask a question regarding RNA seq analysis
I sequenced cells mutated with a single base pair change to follow change in the change in gene expression The thing is when I analyses the data there are loads of gene might be effected by the high expression of the plasmid Shall I analyses the data I have the same way I analyses any gene expression ? Or I should consider the high expression of the gene I introduce with the mutation Or its ok that the introduced gene over express other gene ( that might give us an idea of the gene function and interaction with other gene)

I hope I can find an answer here