Fig. 2.

Identification of time-dependent genes. a Genes that significantly change in expression across time according to spline analysis in the first 8 h (yellow) vs 48 h (blue). b Spline modeling of two genes (Galk and Gale) that undergo gradual expression changes, when using first 48 h (blue) and first 8 h (yellow) compared to the pattern of normalized counts (green). Spline modeling over 8 h misses the main change in pattern. c Spline modeling of two immune genes (AttA and DptB) when using first 48 h (blue) and first 8 h (yellow) compared to the pattern of normalized counts (green). Spline modeling over 48 h smooths out the early impulse signal, drastically changing the inferred expression at time zero (indicated with arrows). d Comparing results from spline analysis (over 48 h in blue and over 8 h in yellow) vs. results from differential expression analysis (|log₂FC| > 1 in green and |log₂FC| > 2 in orange) at FDR < 0.05