Hi,
I have a timeline RNA-seq dataset across four different time points but only for one patient. These four different time points can be annotated as untreated and then three different treatments. I used STAR for the alignment and calculated TPM values using RSEM for further analysis.
I have a couple of questions:
- What is the best way to find the genes apart from using variance/sd/z-score as a metric?
- Is there a way to test these top genes that may be differentially expressed in other diseases or disease-treated settings? Or, something similar to GO or pathway analysis?
Disclaimer: I want to apologize for this post, as this may annoy a lot of statisticians and bioinformaticians. I totally understand that my analysis will be limited, and not much can be interpreted from it. Still, my collaborator, a physician-scientist, is interested in the analysis and totally understands the limitations of the study. We want to pursue it because this is a patient sample, and getting a vast number of patients with the same diagnosis/disease/mutation and then applying similar treatment is not easy.