The former undergrad left us with a set of Edge and DEseq2 analyses of changes in gene expression. I discussed them here last summer (http://rrresearch.fieldofscience.com/2016/08/making-sense-of-rna-seq-comparisons.html). Unfortunately I don't know how to properly interpret them. The former post-doc suggested some analyses, but I'm reluctant to dive into these until I have a better idea of what I'd be getting into.
These analyses are comparing the time-course expression for the wildtype strain against a knockout-mutant strain. So I think they're useful for identifying changes that are dependent on genes whose knockouts we've tested, but not for identifying genes that change for other reasons.
Below is a figure created in a different analysis. This 'cluster' analysis creates subgroups of genes based on how their expression changes between the three sBHI time points or the four transfer-to-MIV time points. Cluster I includes all of the previously identified CRP-S-regulated competence genes except ssb and HI1631, and two other genes, HI1384 and HI1385 (second figure below), which encode ferritin and are reported to be induced when iron levels are high. ssb is consistently induced but usually no more than twofold, so it's lost its 'competence gene' status in this analysis. HI1631 (unknown function) is induced about 10-fold with the typical CRP-S timing, but its maximum expression is quite low and it's put in cluster M.