Hello,

I am a PhD student and am new to RNA sequencing. We recently performed RNA sequencing in the following conditions: 1) WT- Uninfected 2) WT- Infected 3) KO- Uninfected 4) KO- Infected

The gene that we have knocked out is an important metabolic regulator, and has been shown to be crucial in the case of certain infections. The KO cells showed a robust increase in Infectious RNA levels for our pathogen as well. We wish to find the reason for this increase in KO cells, and the role/mechanism of this gene in the context of the infection we are working on.

We have the DEseq excel files for the following comparisons:

• WT-U v WT-I
• KO-U v KO-I
• WT-U v KO-U
• WT-I v KO-I

How should I go about with my analysis? How do I shortlist the genes/pathways that are regulated by my Gene of Interest, resulting in increased infection pathogenesis?

Thank you ```

I recommend for questions about statistical analysis plan to meet with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site for software related questions.