Fig. 1

Gene-expression profiles after sham and PH surgery. a Dendogram of hierarchical clustering of gene-expression profiles for individual post-sham and post-PH samples. The 12,025 Set 1 and Set 2 genes listed in Additional files 3 and 4: Tables S1 and S2 were used in the analysis. Replicate samples are color-coded. Sample numbers represent hours post-treatment unless specified as weeks (W). C, control (no treatment); S, sham; X, PH. Branch lengths correspond to gene-expression differences among samples. The three principal branches are numbered I, II, and III, and set apart with brackets. b Two-dimensional PCA plot for components PC1 and PC2 of samples shown in part a. Samples labeled C, S, and X as in a are shown in green, gray, and red, respectively. The coordinates of replicate samples were averaged and are displayed as single dots; see Supplemental Figure S1D for standard deviations. Arrows indicate the paths followed by the post-sham (gray) and post-PH (red) samples. The S48 post-sham and X48 post-PH time points are highlighted in yellow and the X20 and X44 post-PH time points are connected by a dashed yellow arrow to emphasize the difference between the post-sham S20 to S48 and post-PH X20 to X48 trajectories in the PCA plot. Samples from branches I, II, and III from the hierarchical clustering dendogram (Fig. 1a) are each indicated with dotted circles. c Expression profiles of the mouse core circadian-cycle genes Arntl and Nrd1d1; the corresponding human gene names BMAL1 and RevERBa are given in parentheses. Log2 of RPKM quantifications for averaged replicate post-sham (black) and post-PH (yellow) samples are shown over 72 h; the shaded areas represent standard deviations. The hours post-surgery are shown on the lower x-axis and ZT hours on the upper x-axis