Fig. 3

Diurnal phosphoproteome of mouse liver. a Numbers of phosphosites, phosphopeptides, and phosphoproteins detected in our diurnal phosphoproteome of mouse liver. The distribution of diurnal rhythmic phosphoproteins in the total phosphoproteins. Hierarchical clustering of the cycling phosphoproteins ordered by the phase of the oscillation. Values for each phosphoprotein at all analyzed samples (columns) are color code based on the intensities, low (blue) and high (yellow) z-scored normalized iBAQ. The upper white to black bar indicates the 2 days’ cycle. Daytime is shown in white, while nighttime is shown in black. b Temporal abundance of DNA-binding activity of Bmal1, Clock, Dbp, and Nr1d1/Rev-erbα and their correlated abundance of their phosphorylated forms. X axis represents the sampled time points, Y axis represents the z-scored abundance. c Time-resolved map of signaling cascades regulated by diurnal changed phosphoproteins. Proteins (kinases, phosphoproteins, TFs) were colored based on their peak time, daytime-peaked proteins are yellow (detected in this study) or orange (detected in the study by Robles et al.¹⁰), while nighttime-peaked proteins were blue (detected in the study by Robles et al.¹⁰) or green (detected in this study). Diurnal rhythmic proteins (this study: JTK_CYCLE p < 0.1, Robles et al.¹⁰: q (adjusted p) < 0.1) were shown with red border. Box plots show the path from substrates to pathway-specific TFs were shorter than the path from substrates to all detected TFs (pair tailed Student’s t test p < 0.05). For the box plot, the bottom and top of the box are the first and third quartiles, and the band inside the box is the median of the paths between TFs and substrates