Effects of CF and Arntl KO conditions on the genes oscillating in control liver (control rhythmic data set). (A) Scatterplot showing amplitudes [(maximum − minimum gene expression)/2] in control (x-axis) and CF (y-axis) liver, for all genes in the control rhythmic data set with an amplitude higher than 0.25 in the control condition (1132 of 1627 genes, black and orange dots). The light gray dots represent genes with amplitude lower than 0.25 in control condition (495 of 1627 genes). The red line is the X = Y line, and the blue line is the best fit. The orange dots are circadian-related genes, selected according to gene ontology analysis. (B) As in A but in control (x-axis) and Arntl KO (y-axis) liver. (C) The cutoff on the amplitude was applied for each condition on the control rhythmic data set genes resulting in 1132 of 1627 oscillating genes in control mice, 504 of this same set in CF mice, and 582 of this same set in Arntl KO mice. For each time of the day (indicated as Zeitgebers), the number of genes from the control rhythmic data set with a corresponding phase (time of maximum gene expression) is represented in control, CF, and Arntl KO mice. The radius is equal to the highest number of genes among all three conditions, i.e., 86 genes with a phase between ZT22-ZT23 in the control mice. (D) PAM analysis was performed on the 1132 genes from the control rhythmic data set, and the number of clusters was determined by the best silhouette average. Genes were ranked according to the control condition and normalized by row across all conditions: (white) lowest expression; (red) highest expression. (E) Circular plot showing the phases around the periphery and the amplitudes along the radius. The arrows show the phase and the amplitude of circadian clock gene expression in control (beginning of arrows) and Arntl KO (end of arrows) liver. (F) As in E, but for circadian clock genes in control (beginning of arrows) and CF (end of arrows) liver.
