I have RNA-seq data of a replicated single time-course experiment of a particular microbe with 3 time-points. After running the data in R using maSigPro, I obtained some very interesting expression-vs-time cluster plots. You may take a look at the median plots here. You'll see, for instance, cluster 4 showed what would look like a remarkable spike in expression after the 2nd time point. I understand that genes with similar expression profiles are clustered together which would suggest coordinated expression. I'm guessing my next step will be to pick biologically interesting plots and then "annotate these clusters" someway.
My objective is to find "novel" genes I can further investigate (experimentally) as potential drug targets, hopefully based on these cluster diagrams, so my question is how do I analyze these plots to achieve this? Also, are there other analysis I should perform to further support this hypothesis?
I just started RNA-Seq downstream analysis. I've done some reading (workflows and previous papers) and I've found little clear-cut guiding materials on the subject unique to my problem. Slightly overwhelmed, I am hoping for some direction and correction if I'm missing something.
Thanks for the time family.