Interestingly, many genes change the direction of their regulation between the early and the late phase of the time-course (Figure 1C, Figure S2, Figure S3, Figure S4 and Figure S5).
As a number of genes changed the direction of their regulation between the early and the late phase of the time-course, many categories were represented in both lists.
This synchronous swap of the major functional signatures between the early and the late phase and the fact that the key controllers of the reciprocally regulated processes (as revealed by the network analysis (Figure 4, Figure 5)) are implicated in the mutual repression suggest that the regulatory exchange may occur via tightly controlled reactions, limited to few master regulators.
The massive phase of H2O2-mediated regulation encompassed the time points 15 min and 30 min (1,300 genes controlled, equally distributed between up- and down-regulation), while the late phase occurred between 180 min and 420 min (344 genes controlled, mostly positively), a time period in which most fast-responsive genes had returned to normal expression level (see Additional file 3).
Finally, in the "late" phase (between 36 h and 72 h), most of the mitochondrial aspects studied here were restored to levels comparable to SF. Particularly relevant to notice is that mitochondrial oxygen consumption is reversibly decreased in such a way that addition of the uncoupler FCCP did not restore the respiratory rate to the levels exhibited by SF insects (Figure S1 and S3; Tables 1 and 2).
These findings were difficult to capture in a group analysis as the onset of the late phase varied significantly between cells, indicating that the XO-dependent secondary ROS generation is not homogeneous.
In addition to indicating the degree of initial enhancement, the colour overlay allows differentiation between persistent-, plateau- and washout-type enhancement in the late phase after contrast injection.
However, a difference of net proliferation between the distal and proximal regions is required for the late phase of the limb bud elongation (see below).
Direct comparison between them in the vascular phase is possible, whereas the comparison in the late phase is difficult.
On the other hand, comparisons in the late phase of the disease revealed 4559 genes differentially expressed between MV and NMV patients (P < 0.05, FDR = 0.06).
