What classifying or clustering tools should I apply for an exhaustive gene expression analysis?

Question

[Pin.Bioinf]

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.

Thank you!