Fig. 5

Diurnal proteome of mouse liver. a Distribution of pathway-specific diurnal rhythmic proteins. Yellow, green, and purple cycle represent the number of proteins enriched in lipid metabolism, immunity, and glucose metabolism. Hierarchical clustering of the total (left) and GO specific diurnal rhythmic proteins (right) ordered by the phase of the oscillation. b The bar plot shows the major GO terms enriched by diurnal rhythmic transcripts (yellow), and diurnal rhythmic proteins (green). c The bar plot shows the GO terms enriched by the genes whose diurnal rhythm were inconsistent in transcript and protein level. d Systematic workflow of the ubiquitylation proteome during the circadian cycle in mouse liver. e The total number of ubiquitylated sites and proteins, and the number of ubiquitylation proteins detected at different ZT points. Bar plot shows the comparison between the numbers ubiquitylated proteins with the number of whole-liver proteins detected at different ZT points. f Hierarchical clustering of the ubiquitylated proteins ordered by the phase of the oscillation. g Bar plots show the percentage ratio between ubiquitylated rhythmic TFs and rhythmic TFs versus the percentage ratio between ubiquitylated non-rhythmic TFs and non-rhythmic TFs (left). The percentage ratio between ubiquitylated rhythmic TFs’ TGs and rhythmic TFs’ TGs versus the percentage ratio between ubiquitylated non-rhythmic TFs’ TGs and non-rhythmic TFs’ TGs (right). h The number of ubiquitylated TGs of the diurnal rhythmic TFs versus the number of ubiquitylated TGs of the randomly selected TFs. i Scatterplot shows statistically enriched GO/KEGG pathways by ubiquitylated diurnal rhythmic proteins versus pathways enriched by non-ubiquitylated diurnal rhythmic proteins. j Systematic overview of signal transduction participated by ubiquitylated proteins. Ubiquitylated proteins were colored based on their peak time. Ubiquitylated proteins peaked in the daytime were shown with red border, Ubiquitylated proteins peaked in the nighttime were shown with green border. For all the Hierarchical clustering heatmap, values for each protein 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 diurnal cycle. Daytime is shown in white, while nighttime is shown in black