Table 1.

Workflow Used to Detect Rhythmic, Differentially Rhythmic, and Differentially Expressed Genes in Circadian Transcriptome Data from Livers of Wild-type and Arntl^-/- Mice under Night-restricted Feeding (GSE73552).

Analysis Step	Genes Tested	Method	Variables in Linear Model
1. Rhythmicity	All	RAIN	-
2. Diff. rhythmicity	Rhythmic	LimoRhyde	$\left[\mathrm{1,}{h}_i\mathrm{,}\cos {\mathrm{\theta }}_i\mathrm{,}\sin {\mathrm{\theta }}_i\mathrm{,}{\mathbf{h}}_i\cos \cdot {\mathrm{\theta }}_i\mathrm{,}{\mathbf{h}}_i\sin \cdot {\mathrm{\theta }}_i\right]$
3. Diff. expression	Non-diff. rhythmic	LimoRhyde	$\left[\mathrm{1,}{\mathbf{h}}_i\mathrm{,}\cos {\mathrm{\theta }}_i\mathrm{,}\sin {\mathrm{\theta }}_i\right]$

In the vectors of variables, $h_i$ and ${\mathrm{\theta }}_i$ correspond to genotype (encoded as an indicator variable) and zeitgeber time (in radians) for sample i, respectively. Bold font indicates the variables whose corresponding coefficients were of interest at each step. Arrows indicate that rhythmic genes were tested for differential rhythmicity, and non-differentially rhythmic genes were tested for differential expression.