Hello, I am working on a project and I have already done a differential expression analysis (a simple pairwise comparison with DESeq2).
I have 5 conditions:
- infected with bacteria
- infected with fly
- not infected but exposed to bacteria
- not infected but exposed to fly
- untreated (NAIVE)
For each condition, I have 3 biological samples.
Samples were taken at 2, 7, 14 and 21 days post infection. (I figure I could do a Venn diagram with the genes that are the same in more than one condition, or maybe see the evolution of a gene depending on the time...)
I have many significant genes for each condition, and I would like to know what else I should do (Clustering those genes, or doing a temporal analysis, classification, PCA...) And if there are any examples online, tutorials or articles I could read to start practicing and to start applying to my experiment.